Excessive nitrogen (N) deposition affects aquatic ecosystems worldwide, but effectiveness of emissions controls and their impact on water pollution remains uncertain. In this modeling study, we assess historical and future N deposition trends in Chinese river basins and their contributions to water pollution via direct and indirect N deposition (the latter referring to transport of N to water from N deposited on land). The control of acid gas emissions (i.e., nitrogen oxides and sulfur dioxide) has had limited effectiveness in reducing total N deposition, with notable contributions from agricultural reduced N deposition. Despite increasing controls on acid gas emissions between 2011 and 2019, N inputs to rivers increased by 3%, primarily through indirect deposition. Simultaneously controlling acid gas and ammonia emissions could reduce N deposition and water inputs by 56 and 47%, respectively, by 2050 compared to 2019. Our findings underscore the importance of agricultural ammonia mitigation in protecting water bodies.