Urban estuaries are at risk of increased flooding due to storms and accelerating sea level rise (SLR) caused by anthropogenic climate change. This high and rising risk is forcing coastal communities to develop adaptation strategies. While gray infrastructure (walls, levees, berms) has historically been used to protect coastal communities from flooding, over recent decades nature-based solutions have emerged as a management approach to adapt to increasing flood risk. However, nature-based solutions have yet to be widely treated with the same rigor as traditional engineering solutions, both in hydrodynamic modeling and in policy related to urban planning and flood risk management. This dissertation uses coastal engineering and risk management tools, social and economic data, and stakeholder and practitioner perspectives to assess the utility and limitations of marsh habitat conservation and restoration as a flood defense strategy in the largest urban estuary in California, San Francisco Bay. This suite of research shows that marsh conservation and restoration can be cost-effective paths to reduce coastal flood risk in an era of global climate change and accelerating SLR, providing community safety and co-benefits including improved habitat, carbon sequestration, and recreation opportunities. Results support policy that facilitates conservation and restoration of existing and historical marsh habitat and incorporates habitat and green infrastructure into risk science and insurance.