As part of a larger investigation into potential effects of climate change on estuarine habitats in the Pacific Northwest, we estimated changes in freshwater inputs into four estuaries: Coquille River estuary, South Slough of Coos Bay, and Yaquina Bay in Oregon, and Willapa Bay in Washington. We used the U.S. Geological Surveys Precipitation Runoff Modeling System (PRMS) to model watershed hydrological processes under current and future climatic conditions. This model allowed us to explore possible shifts in coastal hydrologic regimes at a range of spatial scales. All modeled watersheds are located in rainfall-dominated coastal areas with relatively insignificant base flow inputs, and their areas vary from 74.3 to 2,747.6 square kilometers. The watersheds also vary in mean elevation, ranging from 147 meters in the Willapa to 1,179 meters in the Coquille. The latitudes of watershed centroids range from 43.037 degrees north latitude in the Coquille River estuary to 46.629 degrees north latitude in Willapa Bay. We calibrated model parameters using historical climate grid data downscaled to one-sixteenth of a degree by the Climate Impacts Group, and historical runoff from sub-watersheds or neighboring watersheds. Nash Sutcliffe efficiency values for daily flows in calibration sub-watersheds ranged from 0.71 to 0.89. After calibration, we forced the PRMS models with four North American Regional Climate Change Assessment Program climate models: Canadian Regional Climate Model-(National Center for Atmospheric Research) Community Climate System Model version 3, Canadian Regional Climate Model-Canadian Global Climate Model version 3, Hadley Regional Model version 3-Hadley Centre Climate Model version 3, and Regional Climate Model-Canadian Global Climate Model version 3. These are global climate models (GCMs) downscaled with regional climate models that are embedded within the GCMs, and all use the A2 carbon emission scenario developed by the Intergovernmental Panel on Climate Change. With these climate-forcing outputs, we derived the mean change in flow from the period encompassing the 1980s (19711995) to the period encompassing the 2050s (20412065).