Only part of the rain that falls ends up supporting ecosystems or flowing through rivers. Some is used by plants, some evaporates, and some becomes runoff. Yet, how this water is divided across large river systems is still not well understood. In this study, we used stable isotopes (natural tracers in water) and a spatial model to track how rainfall splits into “green” water (used by plants and stored in soil) and “blue” water (runoff, streams, and groundwater) across over 20,000 stream reaches in the Mississippi River Basin. We found that plant transpiration is the dominant way water returns to the atmosphere, while evaporation from soil and open water is much lower than predicted by standard climate models. Although climate strongly affects water partitioning in headwater areas, these differences fade downstream, where river networks appear to smooth out the extremes. This suggests that river basins have a built-in ability to buffer climate variability through how water moves, connects, and is stored. These insights help improve our understanding of water availability and ecosystem resilience as climate pressures grow.