Lee Metcalf National Wildlife Refuge

What We Do


"The mission of the System is to administer a national network of lands and waters for the conservation, management, and where appropriate, restoration of the fish, wildlife, and plant resources and their habitats within the United States for the benefit of present and future generations of Americans" (mission of the National Wildlife Refuge System).

Compatibility determinations are documents written  that signify whether proposed or existing uses of national wildlife refuges are compatible with their establishing purposes and the mission of the National Wildlife Refuge System. Compatibility circles back to the ecological integrity of the System; fragmentation (via non-compatible activities) of System wildlife habitat is a direct threat to the quantity and quality of habitat.

All recreational activities and economic or other uses of a refuge by the public or other non-Service entity require compatibility determinations, which must include our analysis of all facilities, structures and improvements associated with the uses. Economic uses must also contribute to achieving refuge purposes and the mission of the Refuge System. 

Bitterroot River and Riparian Forest

"Riparian areas and wetlands occupy less than 4% of Montana’s land surface, and less than 1% throughout the West, yet they support more than 80% of the bird species found in Montana" (The Bitterroot River Important Bird Area brochure, Bitterroot Audubon, online pdf)

Goal for the Bitterroot River Floodplain and Associated Wildlife

Manage and, where appropriate, restore the natural topography, water movements, and physical integrity of surface water flow patterns across the Bitterroot River floodplain to provide healthy riparian riparian
Definition of riparian habitat or riparian areas.

Learn more about riparian
habitats for target native species and to educate visitors about the benefits of sustaining a more natural floodplain.


The Bitterroot Valley is bisected by the Bitterroot River, which originates in the Anaconda-Pintler Wilderness and the Bitterroot Mountains and flows north to empty into the Clark Fork River near Missoula. Alongside the river are riparian habitats consisting of woodlands (riverfront and gallery forest), scattered grasslands, and wetlands. The riparian woodlands of the Refuge consist of 483 acres of riverfront and gallery forest. The tree community of the 160 acre WVA has been sampled; analysis/report here. The wetland component of the Refuge’s riparian habitat community is 20 acres of oxbows, sloughs, remnants of former gravel pits and creeks—specifically, Barn Slough, Oxbow, North Island Slough, Francois Slough, North Burnt Fork Creek, and Three Mile Creek. Each community has different vegetation and succession requirements.

The Service has identified the habitat needs of a diverse group of target floodplain species, including waterbirds, neotropical migrants, and mammals. Providing for the life history needs of these species will provide the natural floodplain habitat diversity and conditions needed not only for these targeted species, but also for a broad suite of other floodplain associated wildlife. Monitoring will focus on these target species to determine their response to floodplain management actions.

The diversity and productivity of the Bitterroot River Valley at and near Lee Metcalf Refuge was created and sustained by a diverse floodplain surface that was seasonally inundated each spring from both flooding of the Bitterroot River and drainage or seepage from surrounding mountain slopes. Occasional overbank and more regular backwater flooding from the river into its floodplain at the refuge historically helped create and sustain communities and basic ecological functions and values of the site. These flooding processes on the refuge are now restricted by levees along the river, levees and dams on constructed wetland impoundments, roads, the railroad bed, and dams or other obstructions on tributary channels.

To restore the floodplain system at the Lee Metcalf Refuge, restoring the capability of the Bitterroot River to overflow its banks and to back water up tributaries and into other floodplain channels is desirable. The seasonal “pulsed” flooding regime provided uninhibited movement of water, nutrients, sediments, and animal between the river and the floodplain and supported life cycle events and needs of both plant and animal communities. Periodic long-term floods are also important floodplain processes that help maintain community dynamics and productivity. For example, overbank flooding deposits silts and nutrients in floodplains that enhance soil development and productivity. Overbank flooding also creates scouring and deposition surfaces critical for germination and regeneration of riparian woodland species, especially cottonwood. Backwater flooding provides foraging habitat for pre-spawning native fish and rearing habitat for larval and juvenile fishes. Annual backwater flooding recharges water regimes in depressions and shallow floodplain wetlands that serve as productive breeding habitat for amphibians, reptiles, water birds, and certain mammals. Subsequent drying of floodplains concentrates aquatic prey for fledgling water birds. Collectively, the body of scientific evidence suggests that restoring the hydrologic connectivity between the Bitterroot River and its floodplain at Lee Metcalf Refuge is desirable.

The Service will work with engineers and hydrologists to determine the location, design, and steps needed to effectively restore natural waterflow without damaging other refuge resources or neighboring lands. Some of the options include completely removing levees, breaching them, or constructing a spillway to allow water to pass through a specific area.


"Collectively, the many landscape and hydrological changes in the Bitterroot Valley since the Pre-settlement period have dramatically altered the physical nature, hydrology, and vegetation communities of the Lee Metcalf NWR."

Topography and Elevation

Elevations on the Lee Metcalf National Wildlife Refuge range from about 3,230 feet on its north end to about 3,260 feet on its south end at the river. The topographic variation within the refuge is related to the historical channel migrations of the Bitterroot River and its tributaries, scouring and natural levee deposition along minor floodplain channels, and alluvial deposition. A large southeast portion of the Refuge contains higher, more uniform elevations while north and west portions of the refuge have lower, more diverse elevations. Alluvial fans are present in many locations along the Qafy geomorphic surfaces on the east side of the Refuge. A larger tributary fan is present where North Burnt Fort Creek enters the Bitterroot River floodplain; this fan is much larger than the alluvial fans along the floodplain margin that grade into the Sapphire Mountains.    

Geology and Physiography

The following is taken from a report by Heitmeyer, Artmann and Frederickson (2010) describing the geology and physiography of the Refuge: "The Bitterroot Valley, where the Lee Metcalf Refuge is located, is a north-trending basin bounded by the Bitterroot Mountains on the west and the Sapphire Mountains on the east. These mountains and the rich montane Bitterroot Valley date to nearly 90 million years before the present (B.P.). The Bitterroot Valley extends about 120 miles from the confluence of the east and west forks of the Bitterroot River south of Darby to its junction with the Missoula Valley and Clark Fork River 5 miles south of Missoula. The elevation of the valley floor ranges from about 3,900 feet above mean sea level (amsl) in the south to about 3,200 feet amsl near Missoula. Summit elevations of surrounding mountains range from 6,000 to 8,000 feet amsl in the Sapphire Range and exceed 9,500 feet amsl in the Bitterroot Range.

The Bitterroot Mountains are composed of granitic rocks, metamorphic materials, and remnants of pre-Cambrian sediments of the Belt series. The Sapphire Mountains are mostly Belt rocks with localized occurrences of granitic stocks. The unusually straight front of the Bitterroot Range is a zone of large-scale faulting; however, the Bitterroot Valley shows little sign of recent tectonic activity. Undisturbed valley fill shows that tectonic movement since the early Pliocene has been slight or that the entire valley floor has moved as a single unit. The structural basin of the Bitterroot Valley has accumulated a considerable thickness of Tertiary sediments capped in most places by a layer of Quaternary materials. Surficial geology evidence suggests Tertiary fill in the Bitterroot Valley may be up to 4,000 feet thick in some locations. Sediment is coarse colluviums near the fronts of mountains with finer-grain alluvial fill deposits that interfinger with floodplain silts and clays. Channel deposits of the ancestral Bitterroot River lie beneath the valley center.

Low terrace alluvium occurs as outwash, or alluvial fans, below the mouths of tributaries on both sides of the valley. Floodplain alluvium is mostly well-rounded gravel and sand with a minor amount of silt and clay derived from the edges of the neighboring terraces and fans. Most of the refuge is mapped as Qal alluvial deposits of recently active channels and floodplains. These deposits are well-rounded, and sorted gravel and sand with a minor amount of silt and clay. Minor amounts of Qaty (younger alluvial outwash terrace and fan complex deposits from the late Pleistocene) occur next to the Bitterroot Valley alluvium on the north end of the Refuge. Materials in these terraces are well-rounded and sorted gravel of predominantly granitic, gneissic, and Belt sedimentary origin. Qafy surfaces extend along the Bitterroot Valley on both sides of the Refuge. These surfaces are younger (late Pleistocene) alluvial outwash terrace and fan complexes of well-rounded cobbles and boulders in a matrix of sand and gravel deposited in braided-stream environments that formed between and below the dissected remnants of older fans. These surfaces appear to have been at least partly shaped by glacial Lake Missoula, which reached an elevation of 4,200 feet and covered the Bitterroot Valley near the refuge 15,000–20,000 years B.P. during the last glacial advance.

The Bitterroot River has an inherently unstable hydraulic configuration and high channel instability, particularly between the towns of Hamilton and Stevensville. The river reach immediately upstream from the refuge has a complex pattern that is characterized by numerous braided channels that spread over a wide area of the valley bottom. The zone of non-vegetated gravels associated with this main braided channel system has widened and straightened since 1937. In addition to this widening, severe bank erosion is common, but numerous cutoff chutes counteract some lateral bend displacement. Together, active river movements and a braided river channel pattern create low riverbanks and natural levees that encourage chutes and other avenues of river overflow. A complex network of minor channels occurs in the valley floor including the floodplain lands on the refuge. These minor channels appear to flow from ground water discharge, which promotes erosion at slope bases and headwater retreat of small channel head cuts on the floodplain. Channel fragmentation appears to be controlled by irregularities in the respective elevation gradients of the valley.

About 10–15 miles north of Stevensville, the Bitterroot River channel is more confined, compared to its highly braided form farther south. Despite limited changes in river shape north of Stevensville, the river stretch along the Refuge has maintained a highly dynamic, instable channel form due to its geological, topographic, and hydraulic position. The historical floodplain at the Refuge was characterized by the following: (1) multiple abandoned channels (for example, Barn and Francois Sloughs) that were connected with the main river channel during high-flow events; (2) small within-floodplain channels (for example, Rogmans and Swamp Creeks) that received water from ground water discharge and occasional overbank backwater flooding during high-flow events; (3) entry of two mountain- or terrace-derived major tributaries to the Bitterroot River (for example, North Burnt Fork Creek and Three Mile Creek); (4) slightly higher elevation inter-drainage point bars, natural levees, and terraces; and (5) alluvial fans."


"Create the conditions that will allow for the restoration, maintenance, and distribution of native grassland and shrubland species (such as rabbitbrush, needle and thread grass, Junegrass, and hairy golden aster) to provide healthy lands for a diverse group of target native resident and migratory wildlife species and to educate visitors about the historical plant and animal diversity of the valley" (Goal for Grassland and Shrubland Habitat and Associated Wildlife-Refuge CCP).

The Lee Metcalf Refuge’s 1,186 acres of uplands consist of floodplain and terrace grasslands, grassland/shrublands, and shrublands. These communities are defined as having grassland and shrubland species considered facultative or obligate and that usually occur in non-wetland habitats. Historical documents suggest that most higher elevations within the refuge’s floodplain region were covered with grasses and some scattered shrubs. Sites with occasional surface flooding contained more wet meadow or grassland communities interspersed with wetland herbaceous plants (like smartweed), while higher floodplain terraces, slopes, and alluvial fans included both wetland and upland-type grasses (like needle and thread and Junegrass) and shrubs (like rabbit brush and sage). Most floodplain grassland areas have Corvallis, Hamilton, and Grantsdale silt loam and loam soils. Certain small sites in the refuge have saline soils that could have supported more salt-tolerant species. Larger alluvial fans, such as those near Three Mile Creek, are present on “Qafy” surfaces with Lone Rock mixed erosion soils, and these sites historically had a mixed grassland- sagebrush sagebrush
The western United States’ sagebrush country encompasses over 175 million acres of public and private lands. The sagebrush landscape provides many benefits to our rural economies and communities, and it serves as crucial habitat for a diversity of wildlife, including the iconic greater sage-grouse and over 350 other species.

Learn more about sagebrush

The uplands in the valley have historically been disturbed by a variety of land uses since Euro-American settlement in 1841. In 1872 Peter Whaley broke the first sod on what would become the refuge. The primary land use was cattle grazing and, later, agricultural crops (vegetables and grains). Once the refuge was established, the uplands were still disturbed by grazing, farming, haying, and other land practices. Eventually, these grazed and farmed areas were retired and seeded with tame grasses without reseeding of native plant species. These practices greatly altered the land, decreasing overall habitat and animal diversity and increasing the presence of invasive plant species. Most wet meadows have disappeared, and potential saline grasslands are now mostly thistle and wheatgrass. Historical grassy upland terraces no longer contain substantial amounts of native grass or shrubland species. Invasive and other nonnative species now dominate more than 80 percent of refuge uplands. Dominant species now found in those areas include, but are not limited to, cheatgrass, smooth brome, common tansy, mustard species, spotted knapweed, and musk and Canada thistle.

The Service has identified the habitat needs of a diverse group of target upland (grassland and shrubland) species. Providing for the life history needs of these species would provide the natural upland diversity and conditions needed not only for these targeted species but an even greater variety of upland-associated wildlife. Monitoring would be focused on these target species to determine their response to upland management actions.

There are many challenges to restoring the uplands. Restoration would be costly and time consuming. To begin restoration, the refuge would first focus on treating and eliminating invasive species invasive species
An invasive species is any plant or animal that has spread or been introduced into a new area where they are, or could, cause harm to the environment, economy, or human, animal, or plant health. Their unwelcome presence can destroy ecosystems and cost millions of dollars.

Learn more about invasive species
(participate in the annual Refuge Weed Pull) and testing restoration techniques in small patches of tame grassland sites. Since many of these areas do not have irrigation, it may be challenging to germinate some native grassland seed. Many of the upland field soils receive no moisture or shade from the drying sun. This has resulted in a hard soil cap that is almost impossible for native vegetation to take root in and seed successfully. Grazing or disking may help to break up this soil cap to allow for seeding. Lengthier details are contained in the Refuge CCP.


"Where appropriate, manage wetland impoundments to create a diversity of habitats for target waterfowl, shorebirds, and other associated native wetland-dependent species" (Goal for Wetland Impoundment Habitat and Associated Wildlife-Refuge CCP).


Shortly after acquiring the first tract of Refuge land, the Service constructed several impoundments (commonly referred to as ponds) to hold water for migratory waterfowl. These impoundments were mostly built atop agricultural fields. Before this area was homesteaded in the 1870s, these lands consisted of native grassland and shrubland habitats, gallery forests, and some natural streams. Currently, there are 958 acres of wetland impoundments.

The Service has identified the habitat needs of a diverse group of target water bird species, including ducks and shorebirds that use Refuge wetlands. Providing for the life history needs of these species would provide the natural wetland diversity and conditions needed not only for these target species, but also for an even greater variety of wetland-associated wildlife. Monitoring would focus on these target species to determine their response to wetland management actions. In the Bitterroot Valley, the Lee Metcalf Refuge is an important refuge for migratory birds during the spring and fall. Waterfowl breeding and brood rearing occurs on Lee Metcalf Refuge with a great variety of waterfowl using the refuge for these life history requirements; however, the Refuge is not a major production refuge. The most important habitat management efforts would focus on providing optimal habitat for foraging and resting during migration. Lowering the water levels would serve to increase food availability by concentrating foods in smaller areas and at water depths within the foraging range of target wildlife. The rate and timing of drawdowns have important influences on the production and composition of semi-permanent wetland plants and invertebrates that provide protein-rich food resources for each of these target bird species.

Strategies to Attain Goal:
  • Maintain or replace the water management structures in Ponds 1–6, Ponds 8 and 10, and Otter Pond. The remaining wetland impoundment structures will be maintained as needed. 
  • Water level management of all ponds will be changed to a more seasonal water regime that emulates natural increases in distribution and depth in spring, followed by occasional drying in summer and fall to encourage the restoration of wetland and shrub habitat. While drawing wetlands down, exposed shorelines will be monitored and treated to prevent invasive species and monotypic stands of cattails from becoming established. File for changes to existing water rights as directed by the Service’s water resources division. 
  • Prevent invasive species encroachment into newly exposed soil using various mechanical, biological, and chemical treatments to control invasive species and prepare areas for native restoration. 
  • Manage, or maintain, a hemi-marsh condition of the ponds to create a ratio of 50:50 open-water to emergent vegetation (such as bulrush and cattail), providing optimal breeding and brood rearing habitat for diving ducks and dense emergent vegetation over water 2–8 inches deep for bitterns. 
  • Manage or maintain dry ground with tall grasses and mixed herbaceous cover for dabbling ducks. 
  • Emulate long-term patterns of drier conditions in floodplain wetlands in most years including periodic complete drying in some years and occasional prolonged flooding in a few years. 
  • To determine the water-level targets needed to provide adequate food, cover, and nesting substrate for target waterbird species, install staff gauges in all wetland impoundments where they are missing. 
  • Determine the feasibility and methods for restoring the historical flow of the side channel of the Bitterroot River and Three Mile Creek through Ponds 11–13 to restore riparian habitat and reestablish unimpeded flow to the river. 
  • Monitor the trends in abundance and distribution of target species to evaluate the effectiveness of these proposed actions. 

Management and Conservation

Past Actions

 "Many of the water areas of the Metcalf Refuge are surrounded by stands of Ponderosa Pine and Northern cottonwoods. Many of these stands have been killed with the building of the pond areas. These dead stands of trees provide excellent brooding sites for woodduck and hooded mergansers" (1983 Refuge narrative)

After establishment of the refuge in 1964, an extensive system of levees, ditches, and water control structures were constructed to capture and manage the available water supply with a primary purpose of providing migration and nesting habitat for waterfowl. By the late 1980s, more than 1,000 acres had been partially or completely impounded in 14 ponds for managed wetland units. Today, these ponds range in size from 8 acres to more than 200 acres, and their water levels are seasonally managed for waterfowl and shorebirds. Additionally, tributaries and natural springs have been altered by dams or weirs that have allowed the direction or level of surface waterflow to be manipulated. With 24 water claims and 1 water permit, the refuge has the right to 34,209.38 acre-feet of water per year to use for habitat management purposes. The diverted water provides feeding, resting, and nesting habitat for migratory birds, wetland-related wildlife, and other resident wildlife.

Summarized (source: Refuge narratives) the major wetland management and development activities by Refuge staff through the 1990's:

  • Lee Metcalf National Wildlife Refuge was authorized by Migratory Bird Conservation Commission on December 10, 1963.
  • The first parcel was purchased in February 1964.
  • In the mid-1960s, evidence revealed that the west Barn Slough area, a pre-refuge diversion structure structure
    Something temporarily or permanently constructed, built, or placed; and constructed of natural or manufactured parts including, but not limited to, a building, shed, cabin, porch, bridge, walkway, stair steps, sign, landing, platform, dock, rack, fence, telecommunication device, antennae, fish cleaning table, satellite dish/mount, or well head.

    Learn more about structure
    , was sending water through the McPherson and Nickerson Creeks (now Ditches).
  • Ponds 1–4 were completed in the summer of 1966 (refuge files). By 1970, Pond 5 was impounded by forming the existing county road into a levee. Ponds 6, 8, and 10 were constructed between 1967 and 1970, judging from photos from this period.
  • In the mid-1960s, no dikes or structures existed on Francois Slough and North Burnt Fork Creek was unimpeded on the refuge. By 1970, three water control structures were constructed on these waterways, and they remain in place today.
  • Ponds 11–13 were built between 1970 and 1973, as refuge photos show the north ponds in the flood of 1974. Pond E, which was a small impoundment on Rogmans Creek near Pond 11, was likely built around the same time. Pond E was expanded by the creation of Otter Pond in 1989.
  • In the early 1980s, the refuge focused on Three Mile Creek sedimentation issues. This creek flowed into Pond 11 and out through Pond 13 to the river. Two supply ditches were cleaned out in 1985. A bypass channel with three sediment ponds was constructed in 1984 to lead the creek directly to the river. These ponds filled quickly and were cleaned out in 1987.
  • By July 1988, the Pair Ponds were established as part of a rehabilitation project by the Montana Power Company. Pair Ponds comprise 10 acres and are up to 3 feet deep in some areas.
  • Otter Pond was built in 1989 as a solution to the sedimentation of the northern ponds from Three Mile Creek. An 18-inch diameter siphon was constructed to bring water from Pond 10 under Three Mile Creek bypass to supply water to Ponds 11, 12, and 13. This expanded the existing Pond E to about 65 surface acres.
  • In the early 1990s, ditch leveling was completed in Swamp Creek and Ponds 1, 3, 4, 11, and 12.

Restoration Efforts Here for Bull Trout

Fishing opportunity will change in Francois Slough/North Burnt Fork Creek as it undergoes restoration to a cold water fishery. The creek is a mountain and terrace derived tributary to the Bitterroot River. This stream channel has been altered both off and on the refuge through installation of culverts, bridge crossings, and artificial channels and from using the creek to transport water. The refuge has installed water control structures in the WVA to provide fishing opportunities and has impounded water for waterfowl. Undesirable species, such as cattail and reed canarygrass, have formed monocultures along the stream, crowding out and preventing the regeneration of native riparian riparian
Definition of riparian habitat or riparian areas.

Learn more about riparian
vegetation such as cottonwood, willow, and dogwood. Strategic removal of water control structures in the WVA and other areas along the creek will deepen and narrow the streambed. This reconnection will encourage riparian ecological processes to become reestablished. To further encourage riparian habitat restoration, the refuge will plant native vegetation, such as willow and cottonwood, on restored sites. Monitoring water chemistry (temperature, dissolved oxygen, total dissolved solids), streamside vegetation, and target species response will help to determine the success of management techniques.

Refuge Weed Species

"Prevent, reduce, and contain the invasion and spread of noxious, invasive, and harmful nonnative species within the refuge while working with partners to address off-refuge infestations within the surrounding landscape" (Refuge CCP Goal for Invasive and Non-Native Species).

Some species, while not considered noxious by the State of Montana, are considered undesirable and problematic by refuge staff; these include musk thistle, cheatgrass, kochia, reed canarygrass, and teasel.

The refuge has a number of resources to respond to the invasive species invasive species
An invasive species is any plant or animal that has spread or been introduced into a new area where they are, or could, cause harm to the environment, economy, or human, animal, or plant health. Their unwelcome presence can destroy ecosystems and cost millions of dollars.

Learn more about invasive species
problem integrated within national USFWS efforts. The refuge provides office space and other support for one of the Service’s Montana Invasive Species Strike Teams. This team works with refuges throughout the State, including Lee Metcalf Refuge, inventorying and treating new invaders and high priority invasive and nonnative plants. The 2012 report and Refuge treatment map are hyperlinked. Additionally, a partnership with the Ravalli County Weed District has provided several crew members wholly dedicated to treating more established noxious weeds. An annual volunteer weed-pull event for the public occurs, and youth groups like the Montana Conservation Corps, Youth Conservation Corps, and Selway-Bitterroot Foundation interns have also assisted in refuge treatment efforts. Also, invasive species spread and control is integrated into staff fieldwork.

The main planning tool for treating invasives on the refuge is using integrated pest management (IPM). IPM is a structured and logical approach to managing weeds by using a combination of biological, mechanical, and chemical tools. Past IPM efforts have included mapping, treating, and monitoring invasive species on the refuge. Treatment methods for invasives vary with species, daily weather conditions, plant growth stage, and time of year. Methods used to treat invasives have included herbicide application, prescribed fire, biological controls (including goats, flower and root weevils, and flower and root moths), hand pulling, mowing, and cultivating. Along with prescribed burning and grazing, chemical applications of herbicides have significantly aided efforts to control the spread of invasive plant species and possibly the elimination of invasives from specific areas on the refuge. Chemical applications are used on specific species and applied during the optimal plant stage of growth to increase the effectiveness of the application. All chemicals must be approved by the Service for use on refuges, and the application of a specific chemical onsite must undergo a pesticide use proposal evaluation. Approximately 400 acres per year are treated for invasive plants, using chemical applications and mechanical means.

Houndstongue (Cynoglossum officinale)

This is a biennial plant with an extensive taproot. It has 5-petaled reddish-purple flowers branching from a 1-4 foot tall plant. Prioritized by the State as P2B, i.e. abundant and widespread in all counties. 

Montana Dept. of Agriculture has stated that currently in Montana, noxious weed infest about 7.6 million acres (Montana’s Noxious Weed Management Plan, 2008). On the Refuge, Houndstongue (Cynoglossum officinale) plays a significant part in infestation as they grow in dense monotypic stands affecting rangeland, pasture and forest.

Under the Weed Control Act this plant is prioritized P2B, i.e. this weed is abundant and widespread in most Montana counties. Local weed districts are tasked with this challenge: "Management criteria will require containment and suppression where abundant and widespread, and eradication or containment, prevention and education where less abundant" (Montana's Noxious Weeds, Montana State University Extension, 2010). So the Refuge has been working/consulting with the Ravalli County Weed Control District. 

The Refuge is employing all five of the recommended management methods: prevention, herbicide, cultivation, hand-pulling and mowing. During the summer the staff has been actively hand-pulling and digging. Perhaps you have seen our trucks stacked high with houndstongue plants. 

The best time to "dig" these plants is before they set seed. Thereafter, it is really difficult to handle the plant without having the seeds sticking to you, an example of organic velcro. Each plant can produce up to 2,000 seeds that remain viable for 2-3 years in the soil (NRCS).

The Refuge hosts a "Weed Pull" in mid-May specifically for the public to participate in. It is fun and challenging learning of control methods for this weed species and others.

Musk Thistle (Carduus nutans)

This is a biennial plant growing in temperate areas of the world. Found in 40 states of the U.S. A single plant can produce on average 10-11,000 seeds which can stay viable for 15 years! Spreads by seed only. The flower is purple and ball-shaped. Not on the Montana Noxious Weed list, but degree of infestation on Refuge is high.

Kochia (Kochia scoporia)

Kochia is another weed that is undesirable and problematic. It is an annual that thrives in drought years forming monocultures. Not considered noxious by Montana, this plant still has a high degree of infestation on the Refuge requiring management.


 "Create the conditions that will allow for the restoration, maintenance, and distribution of native grassland and shrubland species (such as rabbitbrush, needle and thread grass, Junegrass, and hairy golden aster) to provide healthy lands for a diverse group of target species and to educate visitors about the historical plant and animal diversity of the valley" (Refuge CCP-Goal for Grassland and Shrubland Habitat and Associated Wildlife).

The Service has used cooperative farming and prescriptive livestock grazing in the past as a management tool to manage a variety of upland, riparian, and seasonal wetland habitats. These tools will be used to meet habitat objectives, control vegetative litter, promote native plant production and diversity, control the spread of invasive plant species, and help convert disturbed grasslands back to native plant species.

Grazing by livestock has been a preferred management tool because the effect on habitat is controllable and measurable. Grazing may occur throughout the year as management needs dictate. For wetland units, the purpose of grazing will be to consume portions of emergent vegetation and to break root rhizomes with hoof action. This will likely result in enhanced aeration of soils, removing portions of monotypic emergent vegetation. For upland units, grazing will be used to mimic the historical grazing patterns, most likely employing short-duration, intense grazing pressure with extended rest periods.

Historically, the Bitterroot River Valley was grazed and browsed by native ungulates such as white-tailed deer, mule deer, moose, and elk. Following Euro-American settlement, these valley lands were used for cattle grazing, primarily as winter range as cattle were moved in the fall from the summer grazing and calving locations in the mountain slopes and foothills. Cattle grazing on the refuge grasslands continued until 1975. Between 1993 and 1997 sheep and goats were brought into the refuge in an attempt to control cattails and invasive species; however, prescriptive cattle grazing was not consistently used as a management tool until 2006.

Cooperative farming and prescriptive grazing as habitat management tools are compatible uses on Lee Metcalf National Wildlife Refuge. To ensure consistency with management objectives, the Service will require general and specific conditions for each cooperative farming and grazing permit.

Prescribed Fire

Regional (R6) Fire Management Goals: "to maintain and improve the biological integrity of the region, ensure the ecological condition of the region’s public and private lands are better understood, and endorse sustainable use of habitats that support native wildlife and people’s livelihoods.”

Prescribed burning is a management tool that has been used on the Refuge since 1988 to control some invasive plant species or undesirable monotypic vegetation stands, particularly cattails. It is also used to clear ditches of vegetation that may impede waterflow. One of the most widespread uses of prescribed fire on the Refuge is to rejuvenate grassland vigor.

Since 2004, the refuge has burned 491 acres to improve grassland habitat and 463 acres to improve wetlands. Each year 3–5 acres of ditches are burned to keep them free of vegetation allowing water to travel more freely.

When used properly, fire can accomplish the following:

  • Reduce hazardous fuel buildup in both wildland–urban interface areas and non-wildland–urban interface areas. 
  • Improve wildlife habitats by reducing the density of vegetation, changing the plant species composition, or both. 
  • Sustain or increase biological diversity. 
  • Improve woodland and shrubland by reducing plant density. 
  • Reduce susceptibility of plants to insect and disease outbreaks. 
  • Increase the quantity of water available for municipalities and activities that depend on wildland water supplies. 

Lee Metcalf National Wildlife Refuge will suppress human-caused fires and wildfires that threaten life and property. Appropriate suppression actions—whether aggressive, high intensity, or low intensity—will be based on preplanned analysis, executed to minimize costs and resource losses, and consistent with land management objectives.

Prescribed fire, as well as manual and mechanical fuel treatments, will be used in an ecosystem context to protect both Federal and private property and for habitat management purposes. Fuel reduction activities will be applied in collaboration with Federal, State, private, and nongovernmental partners. For wildland–urban interface treatments, focal areas will be those with community wildfire protection plans and designated communities at risk. The only community at risk near the refuge, as identified in the Federal Register, is the community of Stevensville, Montana. The State of Montana has developed a community wildfire protection plan for all communities in Ravalli County.

All aspects of the fire management program will be conducted in a manner consistent with applicable laws, Department of Interior and Service policies, and guidance established at national, regional, and local levels. Lee Metcalf National Wildlife Refuge will maintain a fire management plan to accomplish the fire management goals described below. Wildland fire, prescribed fire, and manual and mechanical fuel treatments will be applied under selected weather and environmental conditions, monitored using scientific techniques, and refined using adaptive management.


 "Create the conditions that will allow for the restoration, maintenance, and distribution of native grassland and shrubland species (such as rabbitbrush, needle and thread grass, Junegrass, and hairy golden aster) to provide healthy lands for a diverse group of target native resident and migratory wildlife species and to educate visitors about the historical plant and animal diversity of the valley" (Refuge CCP Goal for Grassland and Shrubland Habitat and Associated Wildlife).

The act of restoration involves not only biological communities, but cultural resources (Whaley Homestead) as well. Biologically, a significant part of the restoration proposals is an effort to control invasive plant species and prevent further spread. Grasses and shrubs native to the uplands, including the alluvial fans, are being restored to provide habitat for native wildlife including grassland-dependent migratory birds. Some wetland impoundments may be removed or reduced in size as the river migrates or to provide restoration sites with an overall long-term goal to restore the gallery and riverfront forest for wildlife that are dependent on riparian areas.  


To properly interpret the Whaley Homestead while protecting the structure and visitors, the Refuge needs to determine what level of interpretation is appropriate and then work with partners to restore and interpret this historical homestead based on these guidelines. Very little interpretation has been completed because of its current condition. The structure is not safe enough to allow visitors to regularly walk through the building, despite the resources and time the Refuge and other partners have dedicated to maintaining it. A National Register of Historic Places sign does provide some history of the site. The interior has been updated by the occupants over the years but does not match the period of the late 1800s. To properly interpret this site while protecting the structure and visitors, the Refuge will need to determine what level of interpretation is appropriate and then work with partners to restore and interpret this historical homestead based on these guidelines. To date many refuge partners have expressed enthusiasm and willingness to help restore the site (in part by providing period furniture). Such efforts could ultimately allow visitors to enter this home and interpret the history of early settlers. Nevertheless, these efforts will be costly, and the Service must ensure that this historical structure remains protected. The overarching interpretive theme for the Whaley Homestead will be land use and its effects on wildlife. Topics will include hydrological changes, agricultural practices, grassland conversion, lumber and forest ecology, and native plant usage, all of which have and will continue to affect Refuge resources.  


The 2010 report prepared by Mickey E. Heitmeyer, Michael J. Artmann and Leigh H. Fredrickson entitled An Evaluation of Ecosystem Restoration and Management Options for Lee Metcalf National Wildlife Refuge thoroughly reviewed options for restoration of process (hydrogeomorphic) and habitat. The authors intent: 

"...this report provides information to support The National Wildlife Refuge System Improvement Act of 1997, which seeks to ensure that the biological integrity, diversity, and environmental health of the (eco)system (in which a refuge sets) are maintained. Administrative policy that guides NWR goals includes mandates for: 1) comprehensive documentation of ecosystem attributes associated with biodiversity conservation, 2) assessment of each refuge’s importance across landscape scales, and 3) recognition that restoration of historical processes is critical to achieve goals. Most of the CCP’s completed for NWR’s to date have highlighted ecological restoration as a primary goal, and choose historic conditions (those prior to substantial human related changes to the landscape) as the benchmark condition. General USFWS policy, under the Improvement Act of 1997, directs managers to assess not only historic conditions, but also “opportunities and limitations to maintaining and restoring” such conditions. Furthermore, USFWS guidance documents for NWR management “favor management that restores or mimics natural ecosystem processes or functions to achieve refuge purpose(s)” (USFWS 2001) and to improve biological integrity (USFWS 201:601.FW3).

Given the above USFWS policies and mandates for management of NWR’s, the basis for developing recommendations for Lee Metcalf NWR is the HGM-approach used in this study. The HGM approach objectively seeks to understand: 1) how this ecosystem was created, 2) the fundamental processes that historically “drove” and “sustained” the structure and functions of the system and its communities, and 3) what changes have occurred that have caused ecosystem degradations and that might be reversed and restored to historic and functional conditions within a “new desired” environment. This HGM approach also evaluates the NWR within the context of appropriate regional and continental landscapes, and helps identify its “role” in meeting larger conservation goals and needs at different geographical scales. In many cases, restoration of functional ecosystems on NWR lands can help an individual refuge serve as a “core” of critical, sometimes limiting, resources than can complement and encourage restoration and management on adjacent and regional private and public lands."

Restoration caveats by authors: "Generally, comprehensive restoration of native ecosystems and their sustaining ecological processes at Lee Metcalf NWR will be difficult because of: 1) the small size of the refuge, 2) the “insular” nature of the refuge that increasingly is surrounded by urban/residential expansion and development, 3) highly modified landforms and communities on and adjacent to the refuge, 4) constraints on sustaining the inherent morphology and basic hydrology attributes of the Bitterroot River, and 5) high public use and competing demands for refuge management and access. Despite these substantial challenges, based on the HGM context of information obtained and analyzed in this study, we believe that future management of Lee Metcalf NWR should seek to restore ecological communities and processes to the least degraded state possible, including attempts to: 

  •  Maintain the physical and hydrological character of the Bitterroot River and its floodplain on Lee Metcalf NWR.  
  • Restore the natural topography, water regimes, and physical integrity of surface water flow patterns in and across the Bitterroot River floodplain and adjacent terraces and alluvial fans. 
  • Restore and maintain the diversity, composition, distribution, and regenerating mechanisms of native vegetation communities in relationship to topographic and geomorphic landscape position." 

Water Management

"Where channel migration of the Bitterroot River is occurring, do not inhibit the river from establishing natural flow patterns during high flow events, where appropriate, to enhance existing riparian woodlands and provide suitable restoration sites for both gallery and riverfront forest vegetation that could provide breeding, nesting, feeding, or migration habitat for target species" (Bitterroot River management objective stated in the Refuge CCP, over the next 15 years).

Surface Waters

Lee Metcalf Refuge receives surface water from: tile drain ditches, springs, ephemeral and perennial creeks, subsurface flow, and three lateral irrigation ditches (source majority). The North Lateral Ditch, Middle Lateral Ditch, and South Lateral Ditch are mapped in from the Refuge CCP. These lateral ditches are supplied by the Supply Ditch, a primary canal that carries diverted Bitterroot River water from Victor to just north of the Rrefuge. Surface water entering the refuge from the east often has a high nutrient load as it traverses or drains out of grazed or farmed lands. As a result, the refuge receives nutrient-rich drainage water that results in abundant algal growth during summer months.

The Refuge has a complex system of irrigation ditches, springs, creeks, impoundments, and water control structures for moving water within the refuge to fill the various impoundments and to irrigate upland fields. In 1982, the Refuge submitted 24 water right claims in response to State Senate Bill 76, which mandated adjudication of pre-1973 State water rights. These 24 pre-1973 claims total 31,297.88 acre-feet per year. There is also one post-1973 storage permit (300 acre-feet per year) and two domestic well permits (11.5 acre-feet per year) that increase the total refuge-owned water rights to 31,609.38 acre-feet per year. Most of these rights are supplemental, meaning the water sources are commingled to supply the Refuge needs for optimum operation. In addition, the refuge receives up to 2,600 acre-feet per year (average diversion rate of 8.57 cubic feet per second) from the Supply Ditch Association to augment Refuge water rights. This water flows through three lateral irrigation ditches and costs approximately $4,000 annually. Post-1973 claimed, permitted water rights total 34,209.38 acre-feet per year.

In 2008, the Department of Natural Resources and Conservation of the State of Montana began examining water right claims for the refuge. In this process, a claims examiner reviews various elements to determine the validity and necessity of each claim. A preliminary decree is anticipated to be issued by the water courts in the next few years. After the objection process is completed and the water court is satisfied, the claim representing prior use and a final decree will be issued.

Water is diverted on the refuge to store approximately 2,079 acre-feet of water on 795 acres of wetland impoundments. Water is also used for grassland units on approximately 205 acres. The main season of water use is from mid-March until early December. This varies with water conditions as determined by annual precipitation, snowmelt, and availability of water from the Supply Ditch. Adequate water is important to provide spring and fall migration stopover habitat for migratory birds and for irrigation of habitat restoration sites within upland fields during the summer. During the winter, most impoundments are kept full to provide water for resident species such as bass, aquatic invertebrates, and wintering waterfowl.

Bitterroot River

About 10–15 miles north of Stevensville, the Bitterroot River channel is more confined, compared to its highly braided form farther south. Despite limited changes in river shape north of Stevensville, the river stretch along the refuge has maintained a highly dynamic, instable channel form due to its geological, topographic, and hydraulic position. The historical floodplain at the refuge was characterized by the following: (1) multiple abandoned channels (for example, Barn and Francois Sloughs) that were connected with the main river channel during high-flow events; (2) small within-floodplain channels (for example, Rogmans and Swamp Creeks) that received water from ground water discharge and occasional overbank backwater flooding during high-flow events; (3) entry of two mountain- or terrace-derived major tributaries to the Bitterroot River (for example, North Burnt Fork Creek and Three Mile Creek); (4) slightly higher elevation inter-drainage point bars, natural levees, and terraces; and (5) alluvial fans.

In 1971, the Refuge contracted the placement of riprap material along 1,250 feet of the east bank of the Bitterroot River west of McPherson Ditch (USFWS 1988–93). This riprap was subsequently eroded and moved by high riverflows; by 1984 the riprap was gone, and the bank at this location was moving eastward. Since the mid-1990s, levees built along the Bitterroot River, including the area where the riprap was placed in 1971, have eroded and been at least partly breached in places as the Bitterroot River attempts to move laterally. Also, the Bitterroot River appears to be moving more discharge through the North Island Slough area immediately north of Otter Pond on the north side of the refuge. These river movements could potentially affect the north Otter Pond levee; cause water movement across other floodplain areas on the Refuge; and affect other structures, roads, and the railroad bed.

Our Services

Special Use Permits and Passes

A permit for special authorization from the refuge manager required for any refuge service, facility, privilege, or product of the soil provided at refuge expense and not usually available to the general public through authorizations in Title 50 CFR or other public regulations (Refuge Manual 5 RM 17.6).

Special Use Permits

The Service has developed three different Special Use Permit (SUP) forms which may enable the public to engage in activities considered a) commercial b) research and c) other general uses.

The electronic OMB pdf forms are both the application and the permit. These new forms are available to the public online in a fillable format. It is now possible for prospective permittees to fill out the first pages of the form, print it, sign it, and return it to the refuge for processing. The permit is not valid until approved and signed by a refuge official.

1. National Wildlife Refuge System Commercial Activities Special Use Application and Permit (FWS Form 3-1383-C) for:

  • Commercial activities such as guiding hunters, anglers or other outdoor users; 
  • Commercial filming (audio, video, and photographic products of a monetary value); 
  • Agriculture (haying, grazing, crop planting, logging, beekeeping, and other agricultural products); 
  • Cabins (see also the General Special Use Application and Permit described below); 
  • Trapping. 

2. National Wildlife Refuge System Research and Monitoring Special Use Application and Permit (FWS Form 3-1383-R) for:

  • Research and monitoring activities by students, universities, or other non-FWS organizations.

3. National Wildlife Refuge System General Special Use Application and Permit (FWS Form 3-1383-G)for:

  • Woodcutting; 
  • Miscellaneous events (fishing tournaments, one-time events, other special events); 
  • Cabins/subsistence cabins (depending on the information use requirement, you may need the commercial form); 
  • Education activity; 
  • Other (any activity not mentioned above). 

The above-referenced activities are not necessarily conducted on every refuge. Contact the Refuge manager to inquire whether we consider the proposed use appropriate or compatible on Lee Metcalf National Wildlife Refuge.


Lee Metcalf NWR does not require a pass of any kind to enter or use the Refuge. However, other Refuges may. A series of passes covers the entrance and standard amenity fees charged for using federal recreational lands – including national wildlife refuges:

  • Existing Golden Eagle Passports and National Parks Passes with an expiration date will be honored until they expire. Paper versions of the Golden Age or Golden Access Passports should be exchanged for the new Senior or Access passes. However, plastic Golden Age or Access passes are valid for the pass holder's lifetime and do not need to be exchanged. 
  • The Senior and Access passes are good for the lifetime of the holder and make available (to the pass holder only) 50 percent discounts on some expanded amenity fees. 
  • For the first time, decals and hangtags are available: decals for those who park open-topped vehicles (like Jeeps) or motorcycles at unstaffed federal recreation sites, and hangtags for those who anticipate parking closed vehicles at unmanned facilities. 

Our Projects and Research

Bitterroot River Important Bird Area

"Riparian areas and wetlands occupy less than 4% of Montana’s land surface, and less than 1% throughout the West, yet they support more than 80% of the bird species found in Montana" (text from Bitterroot River IBA brochure-Bitterroot Audubon).

Important Bird Areas (IBA) are a program of BirdLife International. This organization is a partnership consortium of many global conservation organizations. IBA's do one or more of the following:

  • Have one or more globally threatened species
  • Are a site that holds a series of restricted-range species or biome-restricted species
  • Have exceptional large numbers of migratory or congregatory species

Birds are also biodiversity indicators for other animal groups and plants. Though IBA networks are defined by bird fauna, the conservation of IBA sites also ensures the survival of a number of other associated animals and plants.

The National Audubon Society has implemented the IBA program in the U.S. Drilling down from the national level, the Montana Audubon (state Audubon chapter) along with the the local Audubon chapters of the Bitterroot and Five Valley's have played large roles in the application and designation of the Bitterroot River IBA.  

The boundary for this IBA is the 500 year floodplain for the Bitterroot River from the north end of Hamilton to the south side of Lolo. The 30 mile stretch of river designated is dominated by private lands; State land holdings, conservation easements and the Refuge make up the balance of properties contained therein. The key species (out of 240 + species of birds) of the Bitterroot River IBA are also identified and in many cases are priority species, targeted management goals as identified in the Refuge Comprehensive Conservation Plan. Though, the overwhelming highlight of both is the recognition of the value of riparian riparian
Definition of riparian habitat or riparian areas.

Learn more about riparian
and wetland habitat. A Bitterroot River IBA brochure has been developed by Bitterroot Audubon that includes a map and descriptive text. 

Whaley Homestead

"The house and outbuildings retain an excellent level of historic integrity. The historic fabric is largely undisturbed, and much of the original detailing remains. The log understructure, with the weatherboard cladding, pedimented fenestration, and hand carved verge boards reflect accurately the original design and character of this transitional vernacular building….the complex strongly conveys its historic agricultural homestead associations." The nomination form for the National Register of Historic Places designation.

The Whaley Homestead is on the National Register of Historic Places because it exhibits unique qualities of vernacular frontier architecture associated with the beginnings and evolution of agricultural development.   


"The Whaley Homestead was settled in 1877 by Peter Whaley, an Irish immigrant whose family came to the United States in 1841. In 1849, the California gold rush brought him westward. In 1859, Peter Whaley married Hannah E. Whitehead. During the years that followed, Peter Whaley alternated between mercantile activities in the Midwest, and mining in the West. His wife accompanied him on these ventures, and the Whaley's had a total of eight children across the West during the years that ensued. Gold strikes in Montana eventually brought the Whaley's to Bannack in 1863 and Alder Gulch in 1864, where Peter Whaley fared successfully. From there, the family moved to Diamond City in 1866; Peter Whaley dealt supplies to the miners for eight years until the camp played out. From there, Whaley went to the old Jocko Indian agency, where he served as the Agent on the Flathead Indian Agency in Montana from April 1874 to April 1875. In 1875, the Peter Whaley family moved to Hell Gate, and then to the Bitterroot Valley near Florence.

In 1877, Peter Whaley moved his family once more, upon filing a Desert Land claim for this property where he built a small log cabin. The railroad challenged the claim, and for two years Whaley lived on a nearby tract of land, while continuing to cultivate this property. In 1879, Whaley prevailed in his claim, and he "removed [his] House on it?. By 1885, Whaley's homestead proof record cites a major improvement on the property--the substantial house which stands yet today: an eight-room log house, 32' x 48' in dimension. Exterior embellishment appears to have been added by this time. The property was also fenced, and contained a granary, a roothouse and a water ditch. 

David and Julia Whaley, Peter's children, filed homestead claims on adjoining acreage. David claimed an adjoining 160 acres in 1879, Julia filed claim to 80 more acres in 1883. Between the three of them, the Whaley's owned over 400 contiguous acres in section 11. Each made the required improvements - a dwelling and cultivation of the land - although only the Peter Whaley house remains today.

The Whaley's were reportedly not exceptional farmers, in fact, most farms in the Bitterroot turned out to be marginal. Supplementing the farming income, the Whaley's raised livestock and operated a meat market in Stevensville. And much of their livelihood was derived from a sawmill operation in Florence, and the Stevensville Hotel. In 1905, the Whaley's sold their land; Peter Whaley died in 1912.

The homestead changed hands two times before Fred and Anna Hagen bought it in 1921. The Hagens returned the property to a self-sufficient small farm, ripping out the orchard plantings and restoring the production to crops and dairy farming, similar to the original homestead activities. During the 1920's, a cannery was established in Stevensville, and the Hagen's were among the first to raise corn in the valley. For a period they raised hogs. They also ran a small dairy, producing 200 gallons of milk per day in 1926. In 1933-34, the Hagen's built a new milk house; in later years, they grew potatoes and converted the building for cutting french fries. In 1940, Harold Hagen took over the operation of the homestead from his father. All told, Hagen's remained on the land for over 60 years. During the late 1960's and early 1970's, they sold off parcels to the Refuge. Harold Hagen retained life use; he lived there until 1988" (copied from National Register of Historic Places Registration Form - Whaley Homestead [documentation and references included], authors Chere Jiusto and Nathan Latta [State Historic Preservation Office], November 1990).

Management and Future Use

In February 2008, the Montana Preservation Alliance (MPA) received a Preserve America grant from the National Fish & Wildlife Foundation to conduct Interpretive Planning and Stewardship for the Peter Whaley House, an important historical homestead located on the Lee Metcalf National Wildlife Refuge. MPA provided an interpretive framework that recognizes the significant cultural and interpretive values of the Whaley House and the clear potential the homestead offers, to support the mission and federal responsibilities of the Refuge.

2016 Structural Restoration

A competitive bid was won by Betance Inc. to correct several significant issues with the building. Key features addressed included: the foundation, masonry, windows and roofing. Work commenced in April and by July structural concerns were addressed and repaired. 

Law Enforcement

The mission of the U.S. Fish and Wildlife Service is “working with others to conserve, protect, and enhance fish, wildlife, and plants and their habitats for the continuing benefit of the American people.”

Laws and Regulations

All activities on the Lee Metcalf National Wildlife Refuge are subject to state and federal laws, rules, and regulations.
In case of an emergency, call 911