The Pigeon River, a small coolwater stream in western Michigan, has a history of hydrologic, stream habitat, and water quality degradation that led to the loss of its trout population by the late 1980s. After regulatory and watershed management efforts to reduce point- and nonpoint source pollution in the 1990s, the Michigan Department of Natural Resources reinstituted brown trout (Salmo trutta) stocking in 2003. As part of these efforts, we monitored water quality in the Pigeon River each fall between 1996 and 2008, and conducted stream surveys in 2006 and 2007 to evaluate the fish community and outcome of trout stocking. Water quality tended to improve and stabilize through time, although point- and nonpoint source pollution still contributed to water quality problems. Hydrologic instability, caused by wetland drainage, agricultural land use, and irrigation withdrawals from the lower mainstream, created periods of environmental stress. As a result, the fish community of the Pigeon River was dominated by common tolerant warmwater species, typical of agricultural watersheds in southern Michigan. Nonetheless, brown trout surviving from initial stockings in 2003 and 2004 had attained lengths of between 18 and 24 inches by 2007, suggesting the thermal regime, water quality, stream habitat, and forage base of macroinvertebrates and small fish were suitable to maintain a stocked brown trout population. Continued efforts to improve water quality, protect instream habitat, reduce high stormflows, and maintain adequate summer baseflows are needed to fully restore environmental conditions for the native fish community and stocked brown trout in the Pigeon River.