This study provides a new approach to estimate both anthropogenic non-point-source and point-source nitrogen (N) inputs to the landscape, and determines their impacts on riverine ammonia–nitrogen (AN) flux, providing a foundation for further exploration of anthropogenic effects on N pollution. Our study site is Huai River basin of China, a water–shed with one of the highest levels of N input in the world. Multi-year average (2003–2010) inputs of N to the watershed are 27 200 ± 1100 kg N km⁻² yr⁻¹. Non-point sources comprised about 98 % of total N input, and only 2 % of inputs are directly added to the aquatic ecosystem as point sources. Fertilizer application was the largest non-point source of new N to the Huai River basin (69 % of net anthropogenic N inputs), followed by atmospheric deposition (20 %), N fixation in croplands (7 %), and N content of imported food and feed (2 %). High N inputs showed impacts on riverine AN flux: fertilizer application, point-source N input, and atmospheric N deposition were proved as more direct sources to riverine AN flux. Modes of N delivery and losses associated with biological denitrification in rivers, water consumption, interception by dams may influence the extent of export of riverine AN flux from N sources. Our findings highlight the importance of anthropogenic N inputs from both point sources and non-point sources in heavily polluted watersheds, and provide some implications for AN prediction and management.