Long-term monitoring is vital to properly characterize changes in population distribution and abundance over time and can be used to guide management decisions by informing and evaluating the efficacy of management actions. A long-term monitoring initiative for the federally threatened Stephens' Kangaroo rat (Dipodomys stephensi, SKR) was established within Marine Corps Base Camp Pendleton (MCBCP), San Diego, California, USA. From 2005 to 2018, we tracked trends for SKR in: area occupied; relative densities within occupied habitat; and modeled probabilities of occupancy, colonization, and extinction. Both area occupied by SKR and density increased from 2005 to 2018 on MCBCP. Increased area occupied was correlated with increases in estimated density among years, indicating SKR population growth occurs by expansion into suitable habitat patches, as well as increases in numbers within occupied habitat. SKR occupancy was positively associated with gentle slopes (<10%) and moderate open ground (40–80%) and forb cover (>40%). Additionally, probabilities of SKR occupancy and colonization were higher in areas with moderate levels of disturbance. We conclude that long-term occupancy and density monitoring is effective in informing status and trends of spatially dynamic species and that moderate habitat-based disturbance is compatible with the management of SKR.