Water is fundamental to all aspects of human and economic development, so protecting riverine ecosystem is vital. Environmental flow assessment is widely applied to describe how much a river ecosystem changes with alterations to its natural flow regime. This study aimes to assess the environmental flow of Stung Chinit basin, one among the 12 tributaries contributing to Tonle Sap Great Lake, caused by the changes in river flow regimes under future climate change scenarios. Two models were used in this study; SWAT and ERFA, to assess the ecological risk due to flow alterations. The calibration and validation of SWAT model on daily time step for the period of 2000-2009 and 2010-2013, respectively, show good performances based on their statistics indictors (NSE = 0.76, PBIAS = -6.25%, and RSR = 0.48 for calibration; and NSE = 0.81, PBIAS = -23.37%, and RSE = 0.42 for validation). The model was then used to perform the simulation from 3 GCMs (GFDL-CM3, GISS-E2-R and IPSL-CM5A-CC) under two emission scenarios (RCP 4.5 and RCP 8.5) and two time slices (2050s and 2090s). Environmental flow is assessed using ERFA model which calculates the difference in MFRIs between scenario and baseline to derive ERFA classes (no, low, medium and high risks). Overall, the ecosystem of Chinit River might have been affected by the flow alteration as the risk level varied significant across the 3 GCMs of the 2 RCPs for the both time slices. GFDL-CM3 produce highest risk level in high flow while GISS-E2-H and IPSL-CM5A-MR produce higher risk level in low flow. Three GCMs mainly show that the level of risk in 2090s are higher than in 2050s. The change of flow regime under climate change could thread the ecological systems of Stung Chinit river, especially the low flow, which is necessary to take the risk level into account and shall be maintained to minimize the risk.