The saltmarshes inhabited by this small mouse have undergone widespread destruction and degradation, with many filled in for development or agriculture, diked, or used for commercial salt production. Groundwater pumping has also caused subsidence and increased flooding, reducing the extent of pickleweed, while predicted rising sea levels present a further flood risk (1) (2) (4) (8) (9). Most of the marshes have now been reduced to long, narrow strips along outboard dikes, lacking essential vegetation cover on higher ground. Pollution, management for wildfowl, invasive plants such as cordgrass (Spartina), and changes in water quality, such as an influx of fresh water from sewage treatment, have also changed the vegetation composition (1) (3) (4) (7) (8) (12). Finally, within altered marshes, the saltmarsh harvest mouse is at greater risk of predation by domestic cats and non-native red foxes (1) (4), and may suffer competition with the California vole (Microtus californicus) (13).
As a result of these many threats, around 84 percent of the original saltmarshes have now been lost, leaving the saltmarsh harvest mouse restricted to small, often degraded and severely fragmented remnants (1) (7) (8) (9) (14). In addition, the species may now number only a few thousand individuals at most (1) (5) (9), and its small, isolated populations may be at increased risk of inbreeding (1) (9). Subspecies R. r. raviventris is thought to be most at risk of extinction (1) (3) (5) (8) (14).