There is increasing concern about the ongoing reduction in water supplies in the tropical Andes due to climate change effects such as glacier/snow melting resulting from rising air temperatures. In addition, extreme events and population growth are already directly affecting life and water renewability in the country. A countrywide integrated national plan for improving basin-scale water management in Bolivia is needed to assure water availability for agriculture, industry, mining, and human consumption. This study aims to provide a modeling tool to assess Bolivia’s past, current, and future water availability and identify basins at risk of water deficits. The Soil Water Assessment Tool was used to simulate the monthly water balance from 1997 to 2008, as well as the water balance projected to 2050 for the entire country. It considers possible changes in air temperatures and precipitation proposed by 17 Global Circulation Models as well as carbon dioxide projections derived from the Special Report Emission Scenario. Overall, model results were close to satisfactory compared to observations, with some exceptions due to lack of information for expanding the timeline and improving calibration. Based on the calculation of three hydrologic indicators, the study identifies basins that would be the most susceptible to water deficits for a baseline from 1997 to 2008, and in the event of the projected climate change, to 2050.