Summary Market-based watershed protection instruments can effectively improve water quality at various catchment scales. Two payments for watershed services (PWS) programs for water quality improvement have been successively implemented in the Huai River catchment and its sub-watershed, the Shaying River catchment, in Henan Province since 2009. To detect changes in water quality in response to PWS schemes, nonparametric statistical approaches were used to analyze gradual and abrupt trends in water quality, focusing on chemical oxygen demand (COD) and ammonia-nitrogen (NH 3 -N) at 26 monitoring stations in the Huai River watershed during 2006–2013. The nonparametric Mann–Kendall test and the Theil–Sen estimator were used to identify trends and their magnitudes in weekly water quality observations and the Pettitt test was applied to change-point analysis of water quality time series. We found decreasing concentration trends in the weekly water quality data set in this catchment, with water quality at most stations affected by the PWS schemes. The COD and NH 3 -N concentrations decreased at 26 stations by an average of 0.05 mg/L wk and 0.01 mg/L wk, respectively, from 2006 to 2013. Meanwhile, the mean concentrations of COD and NH 3 -N decreased at the 26 stations by an average of 18.03 mg/L and 4.82 mg/L, respectively, after the abrupt change points of the time-series trends of these two pollutants. We also estimated annual reductions in COD and NH 3 -N for each station based on average flow observations using the Theil–Sen approach along with the resulting economic benefits from 2009 to 2010. The COD and NH 3 -N reductions were 14604.50 and 6213.25 t/y, respectively, in the Huai River catchment in Henan Province. The total economic benefits of reductions in these two pollutants were 769.71 million ¥ in 2009 and 2010, accounting for 0.08% and 0.06%, respectively, of the GDP in the entire Huai River watershed of Henan Province. These results provide new insights into the linkages between PWS programs and water quality improvements at regional and local scales for effective management of water resources.