This study aims to assess flow regime alterations under climate change scenarios in the Stung Chinit river basin, one among tributaries of the Tonle Sap Great Lake, Cambodia. Five bias-collected regional climate models (RCMs) under RCP4.5 and RCP8.5 using quantile mapping technique were employed into the Soil and Water Assessment Tool (SWAT) model to quantify changes in future hydrologic characteristic. Three future time horizons —the 2020s, 2050s, and 2080s were assessed in comparison with the baseline period. Based on individual and ensemble average RCMs, the result showed that the average temperature is expected to get warmer between 1°C and 2°C, especially in the 2080s under RCP8.5. The future rainfall indicated variability and an unclear direction, but the dry season rainfall is generally projected to increase for all three future time horizons. Despite this uncertainty, future river discharge at Kampong Thmar in the Stung Chinit basin is still expected to have excessive river discharge between 8% and 144%. This also implies that climate change will induce quite more frequent flood and fewer drought events because of rising in high flow (Q5) and low flow (Q95), respectively. These results will be useful for the Stung Chinit river basin planning, development, and management to cope with future climate change, climate variability and infrastructure development, and relevant implementation activities within the basin and also any future in-depth research