Understanding what drives population dynamics is a key tool for conserving species in fragmented habitats. We evaluate hypotheses explaining fluctuations in populations of flat-tailed horned lizards, Phrynosoma mcallii, in the Coachella Valley, California. This species has the smallest range of any horned lizard in the United States. Within portions of its range, there are potentially conflicting activities, such as suburban development, agriculture, off-road recreation, and activities along the international border. We analyzed fluctuations in populations with respect to resource variables during 2001–2007. Unlike results for other desert lizards, population dynamics of horned lizards did not correlate positively with rainfall. Compaction of sand, abundance of harvester ants, annual rainfall, and annual cover of plants all contributed to parsimonious models, but contributions of these variables varied between year and criteria for the dependent variable (occurrence of horned lizard). We also examined demographic characteristics of increasing and decreasing populations. Rates of growth of hatchlings and age at sexual maturity provided a mechanistic explanation for the observed population dynamics, and were consistent with a food-limiting hypothesis.