Ephemeral wetlands support unique communities dominated by drought-resistant species that persist through dry periods and resilient taxa that recolonize from permanent refuges. Climate change is predicted to reduce the availability of aquatic refuges, likely reducing insect colonization and potentially shifting communities toward dominance by resistant taxa, notably large branchiopods (fairy, clam, and tadpole shrimp). To understand the impacts imposed by this shift, we conducted a mesocosm experiment using rehydrated ephemeral wetland sediment in which tanks were either open or closed to aerial colonization during different seasons. While colonization treatment significantly altered overall community composition due to the addition of insect taxa, large branchiopod community composition remained unchanged. However, we did see entirely different large branchiopod assemblages between spring and summer. Additionally, we observed significant population-level effects on large branchiopods, with differences in body size, abundance, and reproductive maturity between treatments that varied through time and by taxon. Our results suggest that while climate-induced reductions in insect colonization may not immediately alter resistant taxa richness or composition, colonization reduction could fundamentally change resistant taxa populations. These population-level changes may have important implications for ecosystem function and food webs, including impacts on migratory birds that depend on ephemeral wetland productivity. As climate change continues to alter wetland hydrology globally, understanding shifts in cryptic but functionally important ephemeral wetlands becomes increasingly critical for conservation and management.