Agriculture contributes considerably to nitrogen (N) inputs to the world's rivers. In this study, we aim to improve our understanding of the contribution of different crops to N inputs to rivers. To this end, we developed a new model system by linking the MARINA 2.0 (Model to Assess River Input of Nutrient to seAs) and WOFOST (WOrld FOod STudy) models. We applied this linked model system to the Yangtze as an illustrative example. The N inputs to crops in the Yangtze River basin showed large spatial variability. Our results indicate that approximately 6,000 Gg of N entered all rivers of the Yangtze basin from crop production as dissolved inorganic N (DIN) in 2012. Half of this amount is from the production of single rice, wheat, and vegetables, where synthetic fertilizers were largely applied. In general, animal manure contributes 12% to total DIN inputs to rivers. Three-quarters of manure-related DIN in rivers are from vegetable, fruit, and potato production. The contributions of crops to river pollution differ among sub-basins. For example, potato is an important source of DIN in rivers of some upstream sub-basins. Our results may help to prioritize the dominant crop sources for management to mitigate N pollution in the future.