Water quality in the Cuyahoga River, a national heritage river of the United States, has improved greatly since the infamous river fire of 1969, but much of the watershed faces combined demands of a state scenic river valued for nature and the primary water source for surrounding cities. A comparative analysis of mussel abundance was applied to test success between water improvements and mussel assemblages in two similarly sized sub-watersheds, the uper reaches of the Cuyahoga River and an isolated tributary stream, Tinkers Creek, applying multivariate GIS/remote sensing tools and government data resources to contrast variation in lands use, soil types, and potential impacts from impoundments. Mussel populations declined in much of the Upper Cuyahoga River from 1990 to present, while in Tinkers Creek and the West Branch Cuyahoga River, both areas surrounded by residential lands, mussel species changed from a slow water species to species associated with flowing streams. Major structural differences among these stream reaches included regulated flow from reservoirs and consequentially poor soil drainage type in much of the Upper Cuyahoga River, while extensive improvements in Tinkers Creek enhanced flow dynamics and produced well-draining soils. Thus, the mussel assemblages appeared sustained despite a trend towards more human use where water flowed free..