Government‐operated water quality monitoring programmes and their long‐term datasets are crucial to documenting improvements in water resource condition in response to changes in pollutant regulation. We present trends in the biological assessment of water quality (benthic macroinvertebrates) and water chemistry, to determine how these indicators of water quality have responded to shifts in pollutants and regulation in streams and rivers of NY between 1972 and 2012. Change in the results of NYS's multimetric index of biological integrity, the Biological Assessment Profile (BAP) score, was compared between four, 10‐year periods at 30 large river and 138 wadeable stream sites. Water Chemistry trends were analysed through calculation of Weighted Regression on Time, Discharge, and Season from 11 long‐term, large river locations from across NYS. Overall, results suggest small, incremental improvements in biological indicators and a shift from point source dominated pollution to nonpoint sources. From 1972 to 2012, 33% of large river sites sampled improved and 13% declined in biological assessment of water quality, 58% of wadeable stream sites sampled showed no change. Macroinvertebrate community models suggest that impact sources are now dominated by nonpoint nutrient sources. Trends in water chemistry concentrations suggest that ammonia, chloride, total Kjeldahl nitrogen, and total phosphorus had the strongest correlations with time. Total phosphorus and total Kjeldahl nitrogen decreased at base flow and increased during high flows, whereas ammonia decreased across a range of discharges, indicating the shift to nonpoint sources of nutrients and supporting the trends observed in biological indicators.
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