Dramatic increases in global atmospheric N deposition have had adverse effects on inland water ecosystems. China is one of the three hot spots of N deposition in the world. In order to fully understand the impact of N deposition on inland waters in China and formulate a reasonable water pollution treatment plan, we need to clearly quantify the N deposition flux in inland water. Therefore, using the LMDZ-OR-INCA model combined with inland water area data, we obtained the dataset of inland water N deposition in China from the 1990s to the 2010s, which lays a foundation for further understanding the spatial-temporal pattern of inland water N deposition and its impact mechanisms. At the same time, we publicly share this dataset and provide online access and download services at https://ecodb.scidb.cn/detail?dataSetId=892431070195089408.