Disturbance caused by habitat restoration or urbanization can threaten populations of sensitive wildlife species. We examined the effects of habitat disturbance on the ecology of an urban population of Texas Horned Lizards (Phrynosoma cornutum), a species of conservation concern in several states as a result of range-wide declines. We quantified changes in spatial distribution, survival rates, and population size and density over 9 yr (2003–2011) for a P. cornutum population on an urban reserve. The project was divided into three, 3-yr stages based on level of habitat disturbance. Spatial analyses did not support the hypothesis that disturbance associated with restoration activities affected the spatial ecology of P. cornutum on our study site. However, these results were not entirely conclusive due to the logistical constraints of working on a single site with an uncommon species. Survival (n = 147 lizards) was affected by season (inactive-season survival was higher), stage (declining survival in later stages with more disturbance), an interaction of season and stage, and disturbance (covariate of proportion of an individual's home range in disturbed areas for a given year; small negative effect). Major causes of mortality included depredation and anthropogenic activity. We estimated a population size of 33 ± 5 (95% CI of 28–49) individuals (excluding hatchlings) with a corresponding density of 2.68 lizards/ha in 2011, which represented a 38% decline since 2005. This decline was likely a consequence of two factors: the 2008 translocation of 17 adult lizards from an area adjacent to our study site impacted by housing development and a decrease in the annual survival rate of adults over time. Our case study addressed recent calls to examine specific mechanisms by which habitat loss and degradation affect herpetofauna and revealed classic responses of an isolated population to stochastic events and anthropogenic activities.