The biotic integrity of the Florida Everglades, a wetland of immense international importance, is threatened as a result of decades of human manipulation for drainage and development. Past management of the system only exacerbated the problems associated with nutrient enrichment and disruption of regional hydrology. The Comprehensive Everglades Restoration Plan (CERP) now being implemented by Federal and State governments is an attempt to strike a balance between the needs of the environment with the complex management of water and the seemingly unbridled economic growth of southern Florida. CERP is expected to reverse negative environmental trends by “getting the water right”, but successful Everglades restoration will require both geochemical and hydrologic intervention on a massive scale. This will produce ecological trade‐offs and will require new and innovative scientific measures to (1) reduce total phosphorus concentrations within the remaining marsh to 10 µg/L or lower; (2) quantify and link ecological benefits to the restoration of depths, hydroperiods, and flow velocities; and (3) compensate for ecological, economic, and hydrologic uncertainties in the CERP through adaptive management.

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Rising sea levels and temperature will be dominant drivers of coastal Everglades' foundation communities (i.e., mangrove forests, seagrass/macroalgae, and coral reefs) by 2060 based on a climate change scenario of +1.5 °C temperature, +1.5 foot (46 cm) in sea level, ±10 % in precipitation and 490 ppm CO2. Current mangrove forest soil elevation change in South Florida ranges from 0.9 to 2.5 mm year(-1) and would have to increase twofold to fourfold in order to accommodate a 2060 sea level rise rate. No evidence is available to indicate that coastal mangroves from South Florida and the wider Caribbean can keep pace with a rapid rate of sea level rise. Thus, particles and nutrients from destabilized coastlines could be mobilized and impact benthic habitats of southern Florida. Uncertainties in regional geomorphology and coastal current changes under higher sea levels make this prediction tentative without further research. The 2060 higher temperature scenario would compromise Florida's coral reefs that are already degraded. We suggest that a new paradigm is needed for resource management under climate change that manages coastlines for resilience to marine transgression and promotes active ecosystem management. In the case of the Everglades, greater freshwater flows could maximize mangrove peat accumulation, stabilize coastlines, and limit saltwater intrusion, while specific coral species may require propagation. Further, we suggest that regional climate drivers and oceanographic processes be incorporated into Everglades and South Florida management plans, as they are likely to impact coastal ecosystems, interior freshwater wetlands and urban coastlines over the next few decades.