Understanding the effects of climate change is a substantial challenge in estuarine systems because the mixing of freshwater and ocean water adds complexity to climate change projections. Such climate change projections have been conducted in the San Francisco Estuary as part of the U.S. Geological Survey’s CASCaDE Project. In this project, we assessed downscaled air temperature data from 10 Global Climate Change models under 2 Representative Concentration Pathway (RCP) trajectories for greenhouse gas concentrations for three regions of the upper San Francisco Estuary: Suisun and Grizzly Bays, Suisun Marsh, and the legal Delta. We also utilized previously derived regression models to estimate future water temperatures at 16 locations within the upper estuary based on the projected air temperature data.