Abstract: Non-point source pollution is one of the important ecological and environmental problems in the process of green and sustainable development of agriculture. In the process of agricultural production, fertilization and other practices produce excess nutrients not assimilated by crops, which accumulates in the soil and discharged into the river through surface runoff, especially in the rainy season, which is one of the main reasons for the change of river water quality in the basin. It has been reported that different soil utilization methods and cropping systems generate distinct non-point source pollutant profiles, which increases the complexity of agricultural non-point source pollution control to a certain extent. In order to further explore the nitrogen and phosphorus pollution emission characteristics of different crop planting types in farmland, and provide more basic data support for the traceability and control of agricultural non-point source pollution. This study examines agricultural fields under long-term continuous cultivation of different crop types in northern Hebei Province, focusing on their impacts on river water quality within the monitored watershed. Key water quality parameters include Chemical Oxygen Demand (COD), Total Nitrogen (TN), Total Phosphorus (TP), and Ammonia Nitrogen (NH₃-N). The investigation covers three cropping systems: grain crops (maize), vegetable crops (Chinese cabbage), and fruit crops (apricot trees), cultivated across two terrain types: flat land and sloping field. This study compares nitrogen and phosphorus pollution intensities from different crop types and their impacts on regional river water quality by monitoring variations in water quality parameters during distinct flood season phases (early, peak, and late periods). The results indicate that: (1)In terms of temporal distribution, the emission intensity of agricultural non-point source COD, nitrogen, and phosphorus pollution increases with the rise in rainfall during the flood season. (2)In terms of spatial distribution, the background nitrogen level in shallow soil is highest in sloping field, while the background phosphorus level is highest in vegetable cultivation areas. The increase in pollutant emission intensity is most significant in vegetable cultivation areas. Compared to the background index, COD at downstream river sections of vegetable cultivation areas during the flood season increases by approximately 7-fold, and the nitrogen pollution rises by 38.7%. Compared to vegetable crops and fruit crops, grain crops have the greatest impact on TP and COD levels in river water during the flood season. In grain cultivation areas, the increase in TP pollution was nearly 3-fold that of other cultivation areas and the COD increase is nearly 2-fold higher. Additionally, compared with upstream areas, the TN pollution in downstream of grain cultivation areas increases by about 65.3%. (3)In terms of pollutant type distribution, nitrogen pollution intensity in river water during the flood season varies more significantly than that of phosphorus. The dominant water quality pollutants at monitoring sections shift from TP before the flood season to COD during the flood season. The most significant post-flood pollution pattern was nitrogen-phosphorus combined contamination. In summary, the source control and systematic management of agricultural non-point source pollution should prioritize addressing the high nitrogen emission intensity from vegetable cultivation. Key measures—such as optimized fertilization and targeted interception—should be implemented to mitigate the pollution risk of farmland drainage to regional water bodies during flood seasons.