Ottawa Refuge is an excellent location to view bald eagles. There are many nesting eagles on the refuge. The Crane Creek estuary and shallow wetlands provide easy locations for eagles to fish and catch other prey. Many of the eagles on the refuge are immature and have not yet developed the white head and tail feathers of the easily identified adults.

During migration Ottawa Refuge may host as many as 38 different species of warbler including the yellow-rumped warbler. The yellow-rumped warbler is the most versatile forager, so you may find it in a variety of feeding locations. The best time to view these birds is late April through late May as they head north to the coniferous forests to nest. The shrubs along the boardwalk and trails directly behind the visitor center provide excellent views of a variety of warblers and other migratory birds.

An excellent opportunity to view shorebirds at Ottawa Refuge is when the water in Crane Creek is low or when refuge staff lower water levels in pools. This provides mudflats in the spring or fall during peak migration periods. One of the more common shorebird species is the dunlin. These birds stop at the refuge between their Arctic breeding and coastal wintering grounds; flocks as large as 2,000 have been reported in the Crane Creek estuary.

Ottawa Refuge wetlands are managed to provide high quality food and cover for migrating waterfowl, shorebirds, wading birds, and other wetland-dependent wildlife. Permanent and semi-permanent marshes of cattails, smartweeds, bulrush, and other wetland vegetation provide seed, roots, tubers, and aquatic insects for a variety of wildlife essential to a healthy functioning marsh. Refuge staff change water levels during different seasons to provide different types of habitat.

A common plant in coastal wetlands on Ottawa Refuge, cattails provide essential habitat for nesting, feeding, and roosting migratory birds. Dense cattails stands can provide habitat for wintering deer, mink, and muskrats. However, cattails can quickly dominate a wetland reducing the value of the wetland to wildlife. Wetland managers use various management techniques to control cattails, including muskrats. Muskrats feed on cattails and use the plant to construct huts.