Biological reserves are set aside to conserve species in dynamic, human-dominated landscapes; however, most reserve systems protect only small, potentially biased samples of environmental conditions across the range of individual species or habitat types. Such biases can result in counter-intuitive distributions of environmental conditions under combinations of climate change and habitat loss. This study outlines the potential range of interactions and presents a case study investigating vernal pool wetlands in California, USA. The results indicate that future distributions of environmental conditions will be determined as much by land-use decisions as by atmospheric emissions.