Revealing spatiotemporal patterns of fertilizer use and agricultural non-point source pollution in smallholder farming watersheds of mountainous and hilly areas

Mountainous and Hilly Areas (MHAs) are critical for ecological security, water resource conservation, and agricultural production. However, Agricultural Non-Point Source (ANPS) pollution in MHAs remains poorly understood due to the failure of existing models to capture the pronounced spatiotemporal heterogeneity of smallholder farming systems. This study focuses on the Yuanjiang River Basin, a representative subtropical, agriculture-intensive watershed in MHAs, to address both methodological gaps in simulating ANPS pollution and knowledge gaps in understanding its spatiotemporal characteristics. A customized version of the Soil and Water Assessment Tool Plus (SWAT+), referred to as SWAT+ -Smallholder Farming Systems (SWAT+-SFS), was developed to simulate variability within Hydrological Response Units (HRUs) in fertilization timing and dynamic postponement behavior in response to real-time rainfall and soil moisture. Three fertilization representation methods were compared: a conventional discrete-event scheme, a spatially split HRU approach, and the proposed SWAT+ -SFS method. While the split-HRU approach disrupted the hydrological unit structure, SWAT+ -SFS balanced computational efficiency and accuracy. Compared to the conventional discrete-event scheme, the SWAT+ -SFS model reduced overestimation of total nitrogen (TN) during the rainy season and substantially improved total phosphorus (TP) simulation, with average validation Kling–Gupta Efficiency (KGE) values increasing by 67.38 % for TN and 57.03 % for TP across monitoring stations. Simulations revealed that surface runoff-driven losses are significantly amplified by fragmented, prolonged fertilization schedules. This study underscores the critical need to account for complex human behaviors when understanding contemporary watershed hydrological and water quality processes, and highlights the importance of timely, science-based management guidance tailored to smallholder farming systems to support sustainable agriculture in MHAs. • Developed SWAT+ -SFS, an improved SWAT+ model for temporally staggered, rainfall- and soil-moisture-responsive fertilization. • SWAT+ -SFS improved Kling–Gupta efficiency for total nitrogen and phosphorus simulations by 67.38 % and 57.03 %. • Temporally staggered fertilization increased surface runoff-driven nitrogen and phosphorus losses. • Accounting for complex human behaviors is important to modeling modern watershed processes.