The main objective of this study is to assess the SWAT performance for simulating daily water discharge and sediment transport from a catchment of Tonle Sap Lake Basin. The model was calibrated from June 2010 to November 2013 for flow and from June 2011 to November 2013 for sediment. The result showed that the flow simulation was better than that of sediment transport. The model calibration was better during the first hydrological year but lower during the successive years. The model underestimated and overestimated daily water discharge during strong hydrological fluctuations particularly flood events. The statistical performance for flow was satisfactory, with a daily ENS value of 0.50 and an R2 value of 0.53. The sediment calibration was poor. Thus, simulating sediment transport from the catchment where sediment does not follow the discharge trend during flood periods will result in erroneous sediment load estimation. It can be concluded that SWAT may not be able to accurately simulate daily stream flow with strong hydrological variability and daily sediment transport in a catchment where sediment dynamics does now follow the stream flow trend.