As urban development continues to encroach into natural systems, these ecosystems experience increasing degradation to their form and function. Losses in biodiversity and ecosystem function are further compounded by changing climatic conditions. The State of Florida is known for its biodiversity but has experienced declines in species populations and habitats because of urbanization and sea level rise. These declines are particularly challenging in an economy that benefits from a multibillion-dollar income from natural resources tourism. In this study, we assessed the potential future impacts of urbanization and sea level rise on a suite of conservation targets that have been set for the State. We developed six scenarios of all combinations of intermediate and high sea level rise paired with two types of urbanization (sprawling and compact) in both 2040 and 2070 to examine the potential future threats to conservation targets in High Pine and Scrub, Coastal Uplands, and Freshwater Aquatics ecosystems. Our results show projected decreases in extent and area of these priority ecosystems into the future. Florida's current trend in urbanization practices are projected to have a greater impact on conservation targets than if sprawl reduction practices are implemented. Coastal Uplands are projected to experience the greatest loss in area, at up to 47%. Conservation-focused urban planning and climate adaptation strategies can help protect Florida's natural resources with benefits to Florida's tourism economy as well as critical ecosystem functions and services such as coastal flood protection and storm surge risk reduction.