Sea level rise is a fundamental driver of ecosystem change and has the potential to shift the spatial distributions of habitats more rapidly than species can adapt. Rapid sea level rise and associated saltwater intrusion have negative impacts on coastal environments, including loss of habitat for species such as sea turtles and shorebirds. In Florida’s largest wetland, the Everglades, the availability of small fishes that are prey for wading birds serve as an indicator of ecosystem health. In the southwestern part of the ecosystem, sea level rise and a reduction in freshwater flow have converted formerly freshwater marsh into an estuarine mangrove-dominated landscape. In this study, we sampled fish communities in this southwest portion of the Everglades exposed to a range of saline conditions. Biomass of native fishes was highest at a salinity value of approximately 25 parts per thousand, while non-native biomass decreased with increasing salinity. Applying salinity change scenarios, we determined that a 10% reduction from the salinity levels recorded in this study would be optimal for biomass of native fishes. The baseline data we collected on non-native fishes at the site will be useful for monitoring as restoration progresses and for managers working on invasive species control. This region has been actively undergoing ecosystem restoration for the last decade, but restored freshwater flow closer to historical conditions is still years away. Without increased freshwater inflow from hydrologic restoration, rising sea levels and saltwater intrusion may provide conservation challenges for wading birds and their prey-base fishes.