<p>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, reducing insect colonization and potentially shifting communities toward dominance by resistant taxa, notably large branchiopods. To understand these impacts, we conducted a mesocosm experiment using dry wetland sediment in which tanks were either open or closed to aerial colonization during different seasons. While colonization treatment significantly altered overall community composition, large branchiopod community composition remained unchanged, although with different compositions between seasons. 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 taxa. Our results suggest that while climate-induced reductions in insect colonization may not immediately alter resistant taxa richness, they could fundamentally change resistant taxa populations. 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.</p>