The relative importance of agricultural land retirement on water quality and aquatic-community health was investigated in the Minnesota River Basin. Eighty-two sites, with drainage areas ranging from 4.3 to 2200 km2, were examined for nutrient concentrations, measures of aquatic-community health (e.g., fish index of biotic integrity [IBI] scores), and environmental factors (e.g., drainage area and amount of agricultural land retirement). The relation of proximity of agricultural land retirement to the stream was determined by calculating the land retirement percent in various riparian zones. Spearman's rho results indicated that IBI score was not correlated to the percentage of agricultural land retirement at the basin scale (p = 0.070); however, IBI score was correlated to retired land percentage in the 50- to 400-m riparian zones surrounding the streams (p < 0.05), indicating that riparian agricultural land retirement may have more influence on aquatic-community health than does agricultural land retirement in upland areas. Multivariate analysis of covariance and analysis of covariance models indicated that other environmental factors (such as drainage area and lacustrine and palustrine features) commonly were correlated to aquatic-community health measures, as were in-stream factors (standard deviation of water depth and substrate type). These results indicate that although agricultural land retirement is significantly related to fish communities as measured by the IBI scores, a combination of basin, riparian, and in-stream factors act together to influence IBI scores.