Despite more than a century of federal protection, the California sea otter Enhydra lutris nereis remains threatened under the U.S. Endangered Species Act (ESA), and the population has not appreciably expanded its range in two decades. Here, we examine a novel dataset of 725 sea otter live strandings from 1984-2015 to gain insights into demographic and environmental factors underlying threats to sea otter recovery. Using multinomial logistic regression to evaluate spatiotemporal patterns of stranding causes, we demonstrate that increases in stranding rates, particularly outside the range center, are related to a substantial increase in shark bites. By contrast, trauma linked to human activities has declined dramatically, and now accounts for less than 5% of stranding cases. Within the range core, where the sea otter population seems regulated by prey availability, symptoms of energetic stress represent more than 63% of all strandings and are strongly associated with high sea otter density. Conversely, in range peripheries, the majority of strandings are caused by shark bite and neurological disease. Notably, these threats are virtually absent where nearshore habitat is characterized by at least 10% kelp canopy cover. Our analyses reveal that declining kelp cover may therefore constrain the population's spatial expansion and recovery in two key ways. Absence of kelp intensifies density-independent threats in the range peripheries, and likely limits dispersal of reproductive females, which depend on kelp canopy for nursery habitat. These results highlight the significance of both top-down and bottomup processes in population dynamics, and inform an ecosystem-based approach to conservation planning.