The use of water resources has increased with rapid population growth, industrial development, and agricultural activities. Besides, the problem might increase with the potential climate change impacts on water quantity. Thus, sustainable use of water resources becomes crucial. Modeling studies provide scientific support to the analysis of water resource problems and develop strategies for current and potential problems for the sustainable management of water resources. In this study, WEAP-PGM (Water Evaluation and Planning System—Plant Growth Model) was applied to the Sakarya River Basin in Turkey, where almost 50% of the area is agricultural land. The main goals in the study are compiling/integrating available data from different sources in a data-scarce region for hydrological models, and estimating the water budget components of Sakarya River Basin on an annual basis as well as investigating the applicability of WEAP-PGM. General model performance ratings indicated that model simulations represent streamflow variations at acceptable levels. Model results revealed that, runoff is 4747 million m3, flow to groundwater is 3065 million m3 and evapotranspiration is 23,011 million m3. This model setup can be used as a baseline for calculating the crop yields under climate change in the context of water-food-energy nexus in the further studies.