AbstractCurrent integrated modeling frameworks for simulating nutrient sources and dynamics are inadequate for large regional watersheds dominated by groundwater‐surface water interactions due to their simplistic representations of groundwater. In this study, we develop a coupled model that integrates comprehensive surface water, 3‐D groundwater, soil erosion, and nutrient processes. The model is intended to enhance the understanding of nutrient dynamics and sources in the Pearl River Basin (PRB). The model exhibits satisfactory performance in simulating streamflow and sediment transport patterns, capturing essential seasonal variations in water quality indicators. Hydrological budget assessments from 2002 to 2020 in the PRB reveal that 54% of precipitation drains into the South China Sea as surface water, while groundwater discharge as baseflow accounts for 18% of the streamflow. The nutrient budget for the PRB indicates that non‐point sources are the dominant contributors to both nitrogen (N) and phosphorus (P), ranging between 64% and 90%. Improved sewage collection and treatment have reduced point source nutrient contributions over the evaluation period. Groundwater remains a significant and consistent source of N, contributing between 11% and 19%. Natural disturbances and fertilization have led to an upward trend in river N inputs, while afforestation and sewage reduction efforts have resulted in a downward trend in river P inputs. Increased fertilization emerges as a central concern for the PRB, suggesting cost‐effective mitigation of fertilizer usage a pragmatic solution. The coupled simulation model developed in this study offers a novel systems approach for basin‐wide nutrient analysis and pollution control strategies, considering both natural and human‐induced disturbances.