We analyzed the influences of interspecific interactions and environmental factors on rodent community assembly in Mojave Desert wetlands that support the endangered Amargosa vole (Microtus californicus scirpensis). A total of 4927 rodents in six species were captured from 2010 to 2021 within 15 marshes, most frequently including Amargosa voles, harvest mice (Reithrodontomys megalotis), and house mice (Mus musculus), an invasive species. The structure of the community varied considerably over time and by marsh, driven mainly by reductions in harvest mice and increases in Amargosa voles and house mice between 2014 and 2017, and then reductions in Amargosa voles between 2018 and 2021. Northern marshes were dominated by voles, and southern marshes by house mice. Primary determinants of rodent capture rates were interspecific interactions, human proximity, and season. There was a significant inverse relationship between vole and house mouse captures per session, suggesting competitive exclusion. Distance to the nearest town was positively associated with the numbers of voles and negatively associated with the numbers of harvest mice, suggesting that voles may be more sensitive to human disturbance than other rodents. Amargosa voles and harvest mice had annual population cycles with peaks between July and September occurring 6–7 months after rainfall. Our results allow for valuable insight into the influences on community dynamics in desert rodents and highlight that conservation efforts that support Amargosa voles may simultaneously help control house mouse abundance and expansion.