Changes in the catchment scale water balance have important social implications for usable water now and in the future. Stream discharge is also directly related to radionuclides flux in the river water system. The aim of this study was to clarify the water balance in the Chernobyl Exclusion Zone (CEZ) under current and future climate conditions. A catchment scale hydrological model was used with long-term discharge data to project the future trend of radionuclides wash-off from the contaminated catchment at the CEZ in Ukraine. The Sakhan river catchment at the CEZ (51.41°N, 30.00°E) in Ukraine is one of the Pripyat river systems, and has a total surface area of 186.9 km2. We found that under the current climate, 84% of annual input (sum of rainfall and snowmelt) was consumed as evapotranspiration, and discharge was estimated to be 16%. In future climates, annual precipitation is expected to increase. However, a projected increase in the vapor pressure deficit led the consumption of precipitation as evapotranspiration and no significant increase in discharge. The study found that warmer winter and spring temperatures will decrease the snowfall, and increase the rainfall, but it was not enough to increase evapotranspiration. As a result, the peak of discharge shifted from April to March. The increase of future average discharge during the winter and spring came from a combination of (1) increasing rainfall in the winter and spring, and (2) relatively small levels of evapotranspiration, which enhanced the catchment scale water recharge in soil moisture and gave rise to greater discharge during winter and spring. The reduction of extreme river discharge from the hydrological projections could reduce the probability of high radionuclides concentration in the river water system in the future, owing to the reduction of surface runoff water from the contaminated surface soil and/or top layer of floodplain soils in the CEZ.