Kapuas River basin is one of the most important natural water resources in West Kalimantan, Indonesia. However, rapid increasing of forest degradation and land cover changes in the basin and climate variations has decreased the capability of the basin to provide and maintain its functions especially as a water catchment area. Examining the impact of land cover changes and climate variations is required to identify how the on-going and possible land cover and climate change may influence the annual and seasonal discharge, which later can be used to improve the predictability of hydrological consequences in the basin. Large scale of forest degradation and land cover changes had occurred in Kapuas River basin in the period of 1996 to 2006. More than 4,748 km2 (18.9%) of primary dryland forest turned into logged-over forest and around 5,473 km2 (99.1%) of primary swamp forest has been degraded. Hydrological simulation result on August 1997 and December 2007 which represent strong El Nino and La Nina, respectively, shows that the absence of forest cover reduced the discharge up to 15.8% and 38.6% in dry season, and increased the discharge up to 7.0% and 12.5% in wet season. Results of hydrological simulation scenarios revealed that forest degradation and land cover changes affect Kapuas River discharge behavior, even though climate variations are the main factors that contributed to the change of the discharge in both annual and seasonal patterns.