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Excess riverine nitrate causes downstream eutrophication, notably in the Gulf of Mexico where hypoxia is linked to nutrient-rich discharge from the Mississippi River Basin (MRB). We developed a long short-term memory (LSTM) model using high-frequency sensor data from across the conterminous US to predict daily nitrate concentrations, achieving strong temporal validation performance (median KGE = 0.60). Spatial validation—or prediction in unmonitored basins—yielded lower performance for nitrate concentration (median KGE = 0.18). Nonetheless, spatial validation was crucial in quantifying the impact of current data gaps and guiding the model's targeted application to the MRB where spatial validation performance was stronger (median KGE = 0.34). Modeling results for the MRB from 1980 to 2022 showed relatively low riverine nitrate export (19 ± 4% of surplus), indicating large-scale retention of surplus nitrate within the MRB. Interannual nitrate yields varied significantly, especially in Midwestern states like Iowa, where wet-year export fractions (42 ± 24%) far exceeded dry year export (6 ± 6%), suggesting increased hydrologic connectivity and remobilization of legacy nitrogen. Further evidence of legacy nitrate remobilization was noted in a subset of Midwestern basins where, on occasion, annual surplus export fractions exceeded 100%. Interpretable Shapley values identified key spatial drivers influencing mean nitrate concentrations—tile drainage, roadway density, wetland cover—and quantitative, non-linear thresholds in their influence, offering management targets. This study leverages machine learning and aquatic sensing to provide improved spatiotemporal predictions and insights into nitrate drivers, thresholds, and legacy impacts, offering valuable information for targeted nutrient management strategies in the MRB.