AbstractChanges in nitrates are of particular concern in tropical regions undergoing rapid development, as these changes may affect local and downstream riverine ecosystems. This study assessed the spatial and temporal differences in nitrate loads within the Sesan, Srepok, and Sekong (3S) Rivers, the largest tributaries of the Mekong River. Simulation results from a flow and nitrate calibrated SWAT model show large differences in year-to-year nitrate loads, a strong seasonality, and clear variability patterns in monthly nitrate loads in the 3S outlet during the wet season. The annual total nitrate loading from the 3S Rivers account for approximately 30% of the total nitrate load of the Mekong River at Pakse. Nitrate loads during the rainy season accounts for 79% of the total annual load into the Mekong River. The Sesan, Sekong, and Srepok basins have average nitrate yields of 400, 330, and 290kgN/km2, respectively, which is comparable with other forested catchments, but much lower than agriculture dominated catchments in the tropics. Simulations of three future climate scenarios show little variability in annual nitrate loadings under current land use/land cover (LULC), but seasonal difference in nitrate loading during rainy months was observed. Further research is needed to estimate nitrate loads in the 3S basin as influenced by LULC change and dam development, which may potentially result in complex changes to local and downstream riverine ecosystems.