Excessive nutrient exports from the Mississippi/Atchafalaya River Basin (MARB) significantly degrade water quality and lead to the hypoxia zone in the Gulf of Mexico. Quantifying the sources, fate, and transport of nutrients from headwaters to large rivers is critical to diagnose the trend of exported nutrient load and guide efficient and effective conservation planning for nutrient loss reduction. This study investigates the changes in riverine nutrient loads and yields at the HUC12 scale in the MARB from 2001 to 2020. The WRTDS (Weighted Regressions on Time, Discharge and Season) and the SPARROW (SPAtially Referenced Regressions On Watershed attributes) models are integrated to quantify the spatiotemporal patterns and driving factors of riverine nutrient export from the MARB. The integration of the WRTDS model and the SPARROW model allows us to identify and quantify contributions from various sources and examine driving factors for both spatial and temporal variations in nutrient dynamics throughout the MARB. This high-resolution analysis at the HUC12 scale identifies nutrient export hotspots and differentiates areas where nutrient export increases are attributed primarily to anthropogenic activities or hydrological variability. By providing detailed assessments of nutrient source contributions and transport mechanisms, this study offers essential insights for water quality management within the MARB. The identification of local hotspot areas with high and increasing nutrient yields, along with their driving factors at the HUC12 scale, provides crucial local context for targeted conservation strategies to reduce riverine nutrient load in the MARB.