In 1955–1965, the streams and rivers of the upper Susquehanna River basin in New York were surveyed for unionid mussels. We resurveyed unionid populations at the same sites in 1996–1997 to determine whether populations had declined and whether declines could be correlated with inputs of sediments and nutrients from agriculture, which have been thought to be major threats to imperiled unionid populations in North America. Despite widespread evidence of high nutrient and sediment loading from agriculture and other human activities in the upper Susquehanna basin since at least 1965, we found little change in unionid populations between the two time periods. The range of Alasmidonta varicosa contracted while that of Lampsilis cariosa expanded. Overall species richness and the ranges of the other nine species were unchanged. Six species in the basin were formerly listed as Category 2 species or are now considered “Species at Risk” by the United States Fish and Wildlife Service. Of these, Alasmidonta undulata, A. marginata, Strophitus undulatus and L. cariosa are still abundant and widespread in the basin, Lasmigona subviridis is scattered and rarely abundant (but apparently stable) and A. varicosa is rare and declining, perhaps because of hybridization with A. marginata. We caution that improperly designed surveys may erroneously suggest that stable populations are declining.