The San Francisco Bay Area contains a rich array of plant and animal biodiversity and an extensive open space network, embedded within a major metropolitan area. Terrestrial habitats in the San Francisco Bay Area support a wide range of ecosystem services, including carbon storage, forage production, enhanced water supply and quality, crop pollination, and outdoor recreation. The distribution of habitats and plant and animal species is strongly influenced by spatial variation in climate, and is thus expected to change in response to changes in regional and global climate. Current research suggests that most vegetation types will shift toward the coast, especially under scenarios with warmer and drier conditions; range contractions and reduced diversity are projected for California endemic plants in the Bay Area. Bird communities are projected to undergo significant reorganization, leading to altered interactions and community structure. Improved modeling at fine spatial scales represents an important priority to reduce uncertainty in these projections. Climate change is expected to strongly affect ecosystem services. Carbon storage in soils and vegetation could contribute to California’s carbon emissions reduction strategy, but current models project reduced carbon storage in trees due to climate change. Altered agricultural management strategies, including conversion to perennial crops, have the potential to increase soil carbon storage. Climate change impacts on vegetation, hydrology and habitat integrity may negatively affect fire regimes, forage production, water supplies, crop pollination services, and outdoor recreation and quality of life in the San Francisco Bay Area, but few specific projections are available. Strategic conservation planning in the Bay Area is under way to enhance biodiversity conservation through continued open space acquisition. Conservation of heterogeneous landscapes will provide resilience in the face of climate change. Improved understanding of projected climate change impacts on natural habitats will contribute to the development of regional adaptation strategies.