Long-term monitoring programs must use informative yet cost-effective methods. Occupancy estimates that incorporate detection probabilities are used with increasing frequency to describe species status and make management recommendations. Estimating changes in the occupancy of points over time in response to management actions or environmental changes may be especially useful for management of the Palm Springs round-tailed ground squirrel (Spermophilus tereticaudus chlorus), a subspecies covered under the Coachella Valley Multiple Species Habitat Conservation Plan and Natural Community Conservation Plan. In 2002 and 2003, we estimated occupancy and detection probability of ground squirrels across lands modeled as ground squirrel habitat by the Scientific Advisory Committee for the Habitat Conservation Plan and tested a priori hypotheses about how occupancy varied among vegetation and substrate types. In the 2003 study, we asked whether these associations were affected by winter rains after the 2002 drought year. Occupancy in 2003 was estimated at 0.99 (  =  0.01) in Western honey mesquite (Prosopis glandulosa) on dunes and hummocks, and occupancy of the remaining modeled habitat was best described by distance to mesquite, with the occupancy probability decreasing with increasing distance from mesquite on dunes or hummocks. The best-supported model in 2002 described the distribution of ground squirrels as a function of only vegetation and substrate type. However, the best-supported models in 2003 suggested that distance to mesquite was a component of the occupancy of non-mesquite vegetation. Mesquite seems to provide high-quality habitat that can support ground squirrels at high occupancy probabilities that may breed successfully every year. In contrast, other vegetation types provide low-quality habitat that can only support ground squirrels at low occupancy probabilities that may only breed occasionally. Mesquite could be an essential refugium during drought years, and the 4 best-supported models in 2003 suggest that restoration of mesquite beginning near currently occupied mesquite patches could be critical for maintaining ground squirrel populations on the preserves.