Use of the refuge increased around 6,000 years ago, when climatic conditions became wetter and the marsh grew in size. The first documented use of the spring at Refuge Headquarters begins around this time and would continue into the historic period. Inhabitants of the Headquarters site were fishing for tui chub, suckers and squawfish, and were hunting ducks, antelope, mountain sheep, coyote, muskrat and bison. It is during this time period that the historic pattern of seasonal movements to resource areas becomes more apparent in the prehistoric record.

Around 3,500 years ago small villages appear along the edge of the lakes and the Blitzen Valley marshes, and along the Donner und Blitzen River. These sites include either stone ring structures or house pits. Three sites excavated in the Blitzen Valley show increased use of marsh and river resources and a stable way of life. At one of these early villages, rabbit, fish and large game animals were being eaten; grass and juniper seeds were being harvested; and conifer and sage brush were being used to fuel fires. Unfortunately, the inhabitants of this village were forced to abandon their homes when hot cinders from an eruption at Diamond Craters blanketed the landscape.

Around 2,500 years ago the bow and arrow was introduced to occupants of the basin. This new technology greatly increased a hunter’s accuracy. Modification to arrows included blunting the ends so waterfowl could be hunted with the bow and arrow. Before the introduction of the bow and arrow, waterfowl hunting was limited to capturing ducks and coots in long twined nets strung across narrow areas of the marsh. Large numbers of birds could be herded into the nets in the late summer when they molted their flight feathers.

Around 1,400 years ago, the lakes and marshes shrank again, as a drought hit the area. Smaller wetlands meant fewer resources for people, so they used the area less.
The return of moist conditions brought an abundance of lake, marsh and upland resources – and people. As resources increased, so did the number of sites especially around the lakes, in the Double-O area and in the Blitzen Valley. This may be the period of most intensive use of resources in the basin.

Geomorphic data from the Headquarters site suggests that the lake rose significantly 1,050 years ago and again flowed into the Malheur River for a short time before it shrank to its current size. This rise in lake levels forced the inhabitants of the area to move to higher ground around the lakes including shorelines created during older high lake stands. As the lake grew deeper the size of the marsh decreased when the water became too deep to support many marsh plants. As water levels decreased, a greater abundance of marsh resources again became available for humans and wildlife.

But the cycle of wet and dry was to continue. A drought around 700 and then another around 500 years ago again briefly limited the resources available to inhabitants of the basin. As conditions improved, people increased their use of the area, living in stone ring villages in the valley or house pits on the lakes. At the Headquarters site a cache pit filled with seeds from wapato (Indian potato), bulrush and goosefoot attest to the harvest of important plant foods around 400 years ago. The presence of the cached seeds suggests that the site was occupied continuously for several years. Fish bones were found in two fire hearths from this time period, as well as charred sagebrush and willow.

Mat covered shelters, known as wickiups, have been documented during this late period. In historic times these structures were used from late spring through early fall as the Paiute Indians moved to different resource areas to harvest plants and animals. Of particular interest during this late occupation of the basin is the harvest of tui chub at Harney Lake, where roasting pits and garbage piles filled with thousands of fish bones have been excavated. All of similar size, the tui chub were caught in gill nets, then roasted, which preserved them for long term storage.