Global climate change is cumulatively a significant driver of global environmental changes such as flow regime, sediment, and nitrate. Thus, this study aims to estimate changes in sediment and nitrate loads under future climate change scenarios by using SWAT model in Prek Thnot river basin, Cambodia, and a tributary of the Lower Mekong River. The study included three different models (GCMs) under two emission scenarios (RCPs) for two-time horizons which are 2030s (2021-2040 as the medium-term future) and 2060s (2051-2070 as the medium-term future). As the result, the annual baseline sediment load had an average of 0.093 Mt/year and the average annual baseline sediment yield in Prek Thnot river basin is 186 tons/Km2/year. Likewise, for annual nitrate load have around 440 tons/year of each sub-basin and nitrate yield over the watershed has an average of 100 kg/Km2/year. Furthermore, sediment yield rate in this tropical basin is depending on the slope class whereas nitrate yield follows as land use land cover rather than slope class according to our results, sediment yield gets increasing in high-slope and nitrate yield is higher in agriculture areas because nitrate concentration in fertilizer. Under the difference RCPs and GCMs, sediment loads are expected to be monthly affected in May. The change direction (increase/decrease) will be depending on GCMs rather than RCPs and time horizons where sediment ss would be increased from baseline in May for only model RCP8.5GFDL and RCP2.6GFDL while other models expected to decline for both time horizons (2030s and 2060s). However, RCPs and time horizons are expected to determine the magnitude of change. Nitrate loads in May are predicted to decrease for all models, RCPs, and time horizons.