Climate change will affect both sea level and the temporal and spatial distribution of runoff in California. These climate change impacts will affect the reliability of water supplies and operations of California’s water supply system. To meet future urban water demands in the San Francisco Bay Area, local water managers can adapt by changing water supply portfolios and operations. An engineering economic model, CALVIN, which optimizes water supply operations and allocations for the State of California, was used to explore the effects on water supply of a severely warm dry climate and substantial sea level rise, and to identify economically promising long-term adaptations for San Francisco Bay Area water systems. This reconnaissance level modeling suggests that even under fairly severe forms of climate change, Bay Area urban water demands can be largely met, but at a cost. Costs are from purchasing water from agricultural users (with agricultural opportunity costs), more expensive water supply alternatives such as water recycling and desalination, and some increases in water scarcity (costs of water use reduction). The modeling also demonstrates the importance of water transfer and intertie infrastructure to facilitate flexible water management among Bay Area water agencies. The intertie capacity developed by Bay Area agencies for emergencies, such as earthquakes, becomes even more valuable for responding to severe changes in climate.