This report is a collaboration by many state and federal agencies working in the Upper San Francisco Estuary to analyze the potential impacts of climate change to different ecosystems found here. Management stategies for ecological values in the face of climate change require reliable and focused information. In this technical report, our focus is on the Upper San Francisco Estuary (SFE), which contains the Sacramento-San Joaquin Delta and Suisun Bay. This area is home to three interconnected ecosystems: open water, floodplain, and tidal marsh. For this geographical area, we have decades of in-depth monitoring information and scientific investigations that have been successfully used to address a number of management needs. In 2019, the Interagency Ecological Program established a diverse work team to improve our ability to anticipate and respond to climate change impacts. The charge to the group was to:

• synthesize science relevant to climate change,

• determine important knowledge gaps, and

• identify ecosystem metrics for climate change.

We focus our analyses on the likely impacts of climate change on interconnected aquatic habitats. We illustrate how changes in habitats are likely to affect diverse species.

In this report we describe ecological trends attributable to climate change and likely future impacts. We address four principal questions:

1. How have the habitats and biotic communities changed due to climatic trends and events?

2. How are estuarine habitats, flora, and fauna likely to change as climate change trends continue?

3. What are key metrics to document ecosystem change as a result of climate change?

4. How should our monitoring change to improve information value?

Our work builds on the similar work of the San Francisco Baylands Goals Project (Goals Project 2015), which addressed climate change impacts to wetlands downstream of the confluence of the Sacramento and San Joaquin Rivers. We aim to contribute to an integrated baseline understanding of climate change impacts for the entire San Francisco Estuary.