The anticipated impacts of climate change on aquatic biota are difficult to evaluate because of potentially contrasting effects of temperature and hydrology on lake ecosystems, particularly those closed-basin lakes within semiarid regions. To address this shortfall, we quantified decade-scale changes in chemical and biological properties of 20 endorheic lakes in central North America in response to a pronounced transition from a drought to a pluvial period during the early 21st century. Lakes exhibited marked temporal changes in chemical characteristics and formed two discrete clusters corresponding to periods of substantially different effective moisture (as Palmer Drought Severity Index, PDSI). Discriminant function analysis (DFA) explained 90% of variability in fish assemblage composition and showed that fish communities were predicted best by environmental conditions during the arid interval (PDSI <−2). DFA also predicted that lakes could support more fish species during pluvial periods, but their occurrences may be limited by periodic stress due to recurrent droughts and physical barriers to colonization. Zooplankton taxonomic assemblages in fishless lakes were resilient to short-term changes in meteorological conditions, and did not vary between drought and deluge periods. Conversely, zooplankton taxa in fish-populated lakes decreased substantially in biomass during the wet interval, likely due to increased zooplanktivory by fish. The powerful effects of such climatic variability on hydrology and the strong subsequent links to water chemistry and biota indicate that future changes in global climate could result in significant restructuring of aquatic communities. Together these findings suggest that semiarid lakes undergoing temporary climate shifts provide a useful model system for anticipating the effects of global climate change on lake food webs.