Excessive nutrient loss from farmland located on the west bank of Erhai Lake has resulted in significant non-point source pollution within the Lake Erhai basin. However, mitigating this issue proves challenging due to the intricate nature of soil properties and environmental factors. Here, during the rainy season in the Lake Erhai basin, we collected and analyzed soil profile samples, 35 topsoil (0-20 cm) samples, and more than 300 field baseflow samples. Our objective was to explore the influences of soil properties, field baseflow, and agricultural management measures on the spatiotemporal migration of nutrients. The results indicated that the concentration of soil organic matter (SOM) has a significant impact on the spatial patterns of nutrient distribution in sandy soil. Consequently, this leads to a substantial reduction in the potential for nutrient loss in the Lake Erhai basin. The vegetable-field baseflow exhibited the highest concentrations of nitrogen and phosphorus when subjected to high fertilization and flood irrigation. The concentrations of TN and TP in baseflow increase by a factor of 2 and 7.7, respectively, during rainfall compared to periods of no rainfall. Optimizing agricultural measures, such as replacing chemical fertilizers with organic fertilizers and modifying irrigation methods to enhance the organic content of sandy soil and minimize baseflow elution, has a beneficial impact on mitigating agricultural non-point source pollution in the Erhai Lake basin. The research results can enable us to have a more systematic understanding of the problem of non-point source pollution in the Erhai River Basin, and provide a theoretical basis for developing targeted agricultural non-point source pollution mitigation plans. Simultaneously, optimizing agricultural management models to strike a balance between agricultural economic development and ecological protection issues holds significant practical significance for managers.