Knowledge-guided graph machine learning for spatially distributed prediction of daily discharge and nitrogen export dynamics

Spatially distributed prediction of streamflow and nitrogen export dynamics is essential for precision management of agricultural watersheds. While temporal deep learning models such as Long Short-Term Memory (LSTM) have shown strong performance at basin scales, their ability to generalize spatially is limited by insufficient representation of spatial dependencies and flow paths, particularly under data-scarce conditions. To address this gap, we propose HydroGraphNet, a knowledge-guided graph machine learning framework that integrates process-based knowledge and explicit spatial learning into temporal modeling. This framework incorporates directed graph topology to encode watershed connectivity and upstream inflows, with mass balance constraints to improve physical consistency. To enhance generalization in sparsely monitored regions, HydroGraphNet is pretrained on synthetic data generated by the SWAT+ (Soil and Water Assessment Tool Plus). We evaluated HydroGraphNet in the Upper Sangamon River Basin (44 HUC-12 subwatersheds, 2001-2020) against two LSTM baselines: a lumped basin-level model and a distributed variant. When benchmarked on SWAT+ simulations in pretraining, HydroGraphNet improved test NSEs by 8.9 % (discharge) and 13.7 % (NO₃-N load) in temporal extrapolation, and by 27.1 % and 34.7 % in spatial extrapolation, relative to the Lumped LSTM baseline. After fine-tuning with USGS monitoring data, the proposed model achieved mean test NSE (KGE) scores of 0.768 (0.861) for discharge and 0.626 (0.664) for NO₃-N load, substantially outperforming baselines. Attribution analysis further highlighted the importance of upstream inflow representation and graph-based spatial learning in capturing cross-subwatershed dependencies. The model also reproduced seasonal hydrological and biogeochemical patterns consistent with known processes, demonstrating its robustness and process fidelity for spatially distributed prediction. Overall, HydroGraphNet advances the integration of physical knowledge and spatially explicit learning in hydrological modeling, offering a generalizable framework for distributed modeling to support spatially targeted water quality management in data-scarce watersheds.