Recovering species are often limited to much smaller areas than they historically occupied. Conservation planning for the recovering species is often based on this limited range, which may simply be an artifact of where the surviving population persisted. Southern sea otters (Enhydra lutris nereis) were hunted nearly to extinction but recovered from a small remnant population on a remote stretch of the California outer coast, where most of their recovery has occurred. However, studies of recently-recolonized estuaries have revealed that estuaries can provide southern sea otters with high quality habitats featuring shallow waters, high production and ample food, limited predators, and protected haul-out opportunities. Moreover, sea otters can have strong effects on estuarine ecosystems, fostering seagrass resilience through their consumption of invertebrate prey. Using a combination of literature reviews, population modeling, and prey surveys we explored the former estuarine habitats outside the current southern sea otter range to determine if these estuarine habitats can support healthy sea otter populations. We found the majority of studies and conservation efforts have focused on populations in exposed, rocky coastal habitats. Yet historical evidence indicates that sea otters were also formerly ubiquitous in estuaries. Our habitat-specific population growth model for California’s largest estuary—San Francisco Bay—determined that it alone can support about 6,600 sea otters, more than double the 2018 California population. Prey surveys in estuaries currently with (Elkhorn Slough and Morro Bay) and without (San Francisco Bay and Drakes Estero) sea otters indicated that the availability of prey, especially crabs, is sufficient to support healthy sea otter populations. Combining historical evidence with our results, we show that conservation practitioners could consider former estuarine habitats as targets for sea otter and ecosystem restoration. This study reveals the importance of understanding how recovering species interact with all the ecosystems they historically occupied, both for improved conservation of the recovering species and for successful restoration of ecosystem functions and processes.