The impact of climate change is considered to be particularly important in arid environments where ectotherm species constitute the majority of vertebrates. Surprisingly, most studies dealing with the response of reptiles to climate change focus only on a few species. Here, we used a 30‐yr monitoring dataset to assess the consequences of climatic variations on a desert reptile community in eastern Australia. Community structure was measured in three habitat plots differing in flood regime using a range of metrics: the number of individuals and species, alpha biodiversity indices, species turnover, functional diversity, and an indicator describing the change in the critical maximum temperature of the community. Although the functional groups of species sharing similar traits were not clustered by habitat plots, diversity indices were highly plot‐specific. Community composition significantly shifted over time toward higher abundance of individuals for species tolerant to heat in two plots, whereas we found an opposite trend in the third plot. Importantly, the response patterns of the different diversity indices to climatic parameters were not uniform. Yet, water‐related parameters were overall more influential than temperature. A decrease in water availability paired with rising temperatures may have strongly negative impacts. We stress that combining different diversity metrics is critical to better grasp the complexity of community responses to climate change and that predicting future changes in reptile communities of deserts needs to account for the complementarity of different sources of water supply such as those resulting from the dynamics of local rainfalls with flood regime. [ABSTRACT FROM AUTHOR]