Historically, degradation of water quality from mining activity in the Monongahela River Basin adversely affected fish populations in the mainstem river. Improvement of water quality since 1971 has resulted in positive changes in fish populations. We assessed changes in the fishery by analyzing rotenone samples in relation to changes in water quality. Before 1970, pH ranged between 3.8 and 5.8 and alkalinity between 0.0 and 2.0 mg/1. After 1980, mean annual pH ranged from 7.0 to 7.3 and alkalinity ranged from 8.7 to 12.9 mg/1. From 1973 to 1990, mean fish biomass increased in nearly every sample from 41 to 355 kg/ha, Fish diversity also increased. The increase in biomass was significantly correlated with mean alkalinity, but not with mean annual river discharge or mean annual pH.