The area is currently a mix of agricultural land and developed pasture intermixed with fragmented pieces of natural habitat of varying quality. Himalayan blackberry and Reed canary grass are two exotic plants limiting habitat quality in almost all habitat types. Sharecrop and grazing agreements with local farmers and ranchers have been used to maintain habitat for migrating and wintering waterfowl and Sandhill cranes. Corn and small grains are left standing for forage. Eventually these agricultural lands will be restored to wetland habitat.

As a major wintering area for waterfowl in the Pacific Flyway, the Shillapoo supports Canada geese, mallards and other dabbling ducks. Bald eagles nest in adjoining areas and can be present in significant numbers on the wildlife area particularly in winter. Sandhill cranes use the wildlife area and surrounding lands primarily as a staging area during the fall and spring, but a few over-winter in the area. The area also supports mink, great blue heron, black-capped chickadee, western meadowlark, yellow warbler and other species. Listed salmonids found in the Columbia River, Lake River, and Vancouver Lake adjacent to the wildlife area lands include lower Columbia Coho, Chinook salmon, Columbia River Chum salmon, Snake River Sockeye, and Steelhead. Shillapoo is also within the historic range of the Columbian white-tailed deer and Western pond turtle (both state endangered) and is considered potential habitat for both species.