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The Greater Everglades Ecosystem is a globally important ecoregion, home to 68 threatened or endangered species and the largest designated wilderness area in the Eastern United States. Anthropogenic manipulations of the natural hydrology have led to widespread degradation of this ecosystem and monitored population declines across multiple taxa. Simultaneous introductions of hundreds of non-native species into South Florida and their subsequent invasion into the Everglades has further impacted native Everglades communities. Predictions for future climate change suggest that the Everglades is headed towards a drier future, making it crucial to understand how changes in hydrological regimes will impact both native and non-native fauna. Our study combines the results of a landscape-scale experimental manipulation conducted to assess the impact of differing hydrological regimes at the Loxahatchee Impoundment Landscape Assessment between 2018 and 2020 with a community composition analysis of data collected across multiple habitat types throughout Everglades National Park between 2000 and 2002. Both datasets used a variety of survey methods to extensively characterize the amphibian and reptile amphibian assemblage across habitat types and hydrological regimes. An NMDS analysis indicated that variation in hydrology is the primary axis structuring reptile and amphibian habitat usage across the Everglades, with non-native species more likely to be indicators of drier habitat types. This result concurred with those from the landscape-scale manipulation, in which non-native species were significantly favored by drier hydrological conditions. Taken together, these results suggest that a drier future within the Greater Everglades Ecosystem may facilitate further spread of South Florida’s diverse non-native amphibian and reptile assemblage.