► We separate the impacts of three climate change factors on water supply in California. ► We provide another approach to reduce uncertainties in the impact estimate. ► Annual runoff change is the most dominant factor in the middle of this century. ► Sea level rise becomes the most critical factor in the end of this century. ► Seasonal runoff shift will add to but not dominate climate change impact. A 3-step perturbation ratio method is designed to facilitate the separation of seasonal pattern shifts of inflow to reservoirs from 2 other climate change factors: annual inflow change and sea level rise. The modeled region provides source water for the State Water Project and Central Valley Project of California. Four groups of the water planning simulation model CALSIM II run are implemented to isolate individual impacts of seasonal pattern shift of inflow to reservoirs, annual inflow volume change, and sea level rise on water supply in this region. Estimates of climate change impacts on water supply are made for the middle and end of the 21st century. These impacts are in terms of the ensemble means of CALSIM II simulation results for each of 12 climate model projections under the A2 or B1 emission scenario. The results indicate that around the middle of this century annual inflow changes contribute most to climate change impacts on water supply. But near the end of the century sea level rise of 61 cm in San Francisco Bay plays a major role in affecting water supplies.