Geostatistical analyses of 35 plant species from 213 packrat middens with combined records spanning the last 40,000 yr indicate that many presumed winter precipitation-dependent taxa that existed in the Sonoran Desert during the last glaciation were expelled by increasing monsoon precipitation instead of waning cool-season moisture. The statistical influence of excessive monsoon rainfall on the distributions of many species probably reflects the simultaneous increase in the magnitude and occurrence of fire. During the early Holocene, results indicate a dramatic decrease in cool-season precipitation and an increase in monsoon rainfall. Levels of temperature and precipitation continued to change linearly until they reached modern values. These conclusions are drawn from a newly developed computer model that determines which climatic factors impede species movement into an unoccupied region. Climatic “limiters,” derived from digital versions of modern plant distributions, elevation, and meteorological data, formed the basis of the reconstructions. Particularly important distribution limiters for the Sonoran Desert include maximum warm-season precipitation and low winter temperatures. The model allows for quantitative estimates of past climatic changes with relatively detailed temporal and spatial resolutions. These results can be used to refine paleoclimatic interpretations based on coarser resolution General Circulation Models.