Sedimentation has been identified as one of the major causes of habitat degradation of backwater areas of the upper Mississippi River. Sedimentation (deposition of river carried soil and sand) decreases water depth which encourages nuisance growths of aquatic vegetation which may result in stagnation and oxygen depletion. To survive, fish must move out of such stagnated backwaters; however, little was known of fish behavior during low-oxygen periods.

In 1985 a radio telemetry study was conducted on largemouth bass in Pool 12 to learn more about habitat use, spawning habitat requirements, and response of these fish to periods of anoxic conditions during both the summer and winter periods. Radio tagged largemouth bass were relatively sedentary during the summer and winter but moved up to nine miles during the spring and fall. Most radio tagged bass occupied the same summer and winter sites in consecutive years, although these sties were widely separated. It was determined; though, that the severe sedimentation problem associated with the backwater areas, there were few areas in Pool 12 that could serve as wintering habitat for largemouth bass, crappie, bluegill, and other centrarchids. It was determined that this loss of habitat was the limiting factor of these populations and that this decline would continue without some sort of intervention.

In order to sustain and increase these populations of fish, backwaters needed to be rehabilitated by increasing water depth and ensuring an adequate supply of oxygenated water during the winter period. The Environmental Management Program (EMP) allowed for backwater and habitat rehabilitation. Selected backwaters were dredged to increase water depths and water control structures were installed to provide oxygenated water when needed. Brown's Lake, Pool 13, was one of the first backwater areas to benefit from this research. There has been a considerable number of other EMP projects designed in a similar fashion to the Brown's Lake project. Similar sites include Big Timber (Pool 17), Bussy Lake (Pool 10), McCartney Lake (Pool 11), and Potters Marsh (Pool 13).