The aquatic landscapes of the Sacramento–San Joaquin Delta (hereafter, the Delta) and Suisun Bay represent both a significant past and future soil carbon stock. Historical alterations of hydrologic flows have led to depletion of soil carbon stocks via emissions of carbon dioxide (CO2), and loss of elevation as a result of subsidence. Optimizing ecosystem hydrology in the Delta and Suisun Bay could both reduce and reverse subsidence while also providing significant opportunities for climate mitigation and adaptation. Emissions of greenhouse gases (GHGs)—notably CO2, methane (CH4 ), and nitrous oxide (N2O)—contribute to global warming at different rates and intensities, requiring GHG accounting and modeling to assess the relative benefits of management options. Decades of data collection, model building, and map development suggest that past and current management actions have both caused—and can mitigate—losses of soil carbon. We review here the magnitude of potential GHG offsets, management options that may be achievable, and trade-offs of carbon storage under different land management. Using a land-use/land-cover framework to assess these management options, we describe the potential of three interventions (impoundment to reverse subsidence, agricultural management, and tidal reintroduction and/or maintained connectivity), both in acreage and radiative balance to clarify their relative influence on the region’s GHG balance today and in relation to its millennial history. From floodplains to farming to floating aquatic vegetation, we find specific scalable strategies to manage hydrology that can alter regional GHG balance. Preservation of soil carbon stocks and restoration of net atmospheric CO2 fluxes into soils are the primary route to net negative emissions in the Delta and Suisun Bay, with CH4 emission management occurring in a supporting role. Over a 40-year horizon of climate-mitigation markets, the resilience of different aquatic habitats introduces the most uncertainty, from expected and unexpected hydrologic changes associated with land, ocean, and operational water flows.