Accurate identification of dissolved reactive phosphorus (DRP) sources and quantification of its loading into aquatic environments are critical for mitigating eutrophication and improving environmental management strategies. DRP, the most bioavailable form of phosphorus, stimulates algal proliferation directly, serving as a major driver of eutrophication, thereby threatening water quality degradation and freshwater sustainability. However, quantifying DRP loads and tracing their sources remains challenging due to landscape heterogeneity and the dynamic nature of precipitation events. In this study, a daily time-step DRP transport model was constructed for the entire Yamato River catchment (1077 km2), utilizing the Soil and Water Assessment Tool. A total of 106 weekly water quality samples, collected from January 2023 to December 2024, were analyzed for DRP concentrations and used for model calibration and validation. Results reveal that DRP fluxes are predominantly event-driven, with peak discharges closely associated with intense rainfall events. Non-point source (NPS) DRP loading, particularly from agricultural fields, was observed during rainfall, regardless of soil type or phosphorus adsorption capacity. These NPS contributions affect ecosystem vulnerability and closely correlate with environmental stability. Scenario analysis demonstrates that implementing deep fertilization practices can reduce annual NPS DRP loading by approximately 32% and lower peak loads during rainfall events by 28%. This study enhances the understanding of NPS DRP dynamics by identifying specific landscape characteristics linked to eutrophication risk, providing essential scientific guidance for targeted mitigation strategies. These findings are particularly important for enhancing the accuracy and effectiveness of environmental management strategies in the context of future climate change.