Large-scale deforestation alters water availability through its direct effect on runoff generation and indirect effect through forest-climate feedbacks. However, these direct and indirect effects and their spatial variations are difficult to separate and poorly understood. Here, we develop an attribution framework that combines the Budyko theory and deforestation experiments with climate models, showing that widespread runoff reductions caused by the indirect effect of forest-climate feedbacks can largely offset the direct effect of reduced forest cover on runoff increases. The indirect effect dominates the hydrological responses to deforestation over 63% of deforested areas worldwide. This indirect effect arises from deforestation-induced reductions in precipitation and potential evapotranspiration, which decrease and increase runoff, respectively, leading to complex patterns of runoff responses. Our findings underscore the importance of forest-climate feedbacks for improved understanding and prediction of climate and hydrological changes caused by deforestation, with profound implications for sustainable management of forests and water resources.