Abstract: Non-point source pollution is an important ecological and environmental problem in the green and sustainable development of agriculture. During agricultural production, fertilization and other practices produce excess nutrients not assimilated by crops, which accumulate in the soil and are discharged into the river through surface runoff, particularly during the rainy season. This a primary reason for changes in river-water quality in the basin. Different soil utilization methods and cropping systems have been reported to generate distinct non-point source pollutant profiles, which increases the complexity of agricultural non-point source pollution control to a certain extent. To further explore the nitrogen and phosphorus pollution emissions characteristics of different crop-planting types in farmlands and provide more basic data for the traceability and control of agricultural non-point source pollution, this study examined agricultural fields under long-term continuous cultivation of different crop types in northern Hebei Province, focusing on their impact on river-water quality within the monitored watershed. The key water-quality parameters included the chemical oxygen demand (COD), total nitrogen (TN), total phosphorus (TP), and ammonia nitrogen (NH3-N). The investigation covered three cropping systems, grain (maize), vegetables (Chinese cabbage), and fruit (apricot trees), cultivated across two terrain types: flat land and sloping fields. This study compared the nitrogen and phosphorus pollution intensities of 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 emissions intensity of COD, nitrogen, and phosphorus pollution increased with an increase in rainfall during the flood season. 2) In terms of spatial distribution, the background nitrogen level in shallow soil was highest in sloping fields, whereas the background phosphorus level was highest in the vegetable cultivation areas. The increase in pollutant emissions intensity was most significant in the vegetable cultivation areas. Compared to the background index, the COD in the downstream river sections of vegetable cultivation areas during the flood season increased by approximately seven-fold, and nitrogen pollution increased by 38.7%. Compared to vegetables and fruit, grain crops had the greatest impact on the TP and COD levels in river water during the flood season. In grain cultivation areas, the increase in TP pollution was nearly three-fold that in other cultivation areas, and the COD increase was nearly two-fold higher. Additionally, compared to the upstream areas, TN pollution downstream of the grain cultivation areas increased by 65.3%. 3) In terms of pollutant type distribution, the intensity of nitrogen pollution in the river water during the flood season varied more significantly than that of phosphorus. The dominant water-quality pollutants in the monitoring sections shifted from TP before the flood season to COD during the flood season. The most significant post-flood pollution pattern was combined nitrogen–phosphorus contamination. In summary, source control and systematic management of agricultural non-point source pollution should prioritize addressing the high nitrogen emissions 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 the flood season.