Mangrove restoration efforts often focus on planting seedlings and ignore the underlying physical parameters causing mangrove loss, such as disruption to the hydrological regime. In order to determine success of hydrological restoration, baseline data need to be collected and assessed from a degraded mangrove system undergoing hydrological restoration. Sample collection occurred within the Rookery Bay National Estuarine Research Reserve, FL along a gradient of deforestation, from a heavily degraded dead (no canopy) zone to a transitional zone, and into a full canopy zone and compared to a natural (reference) full canopy mangrove environment nearby. Data included faunal abundance and diversity, stable isotope (carbon and nitrogen), and a suite of environmental variables, such as salinity, temperature, dissolved oxygen and grain size. These baseline data provide critical information on the ecosystem functioning that can be used to track community changes in mangrove habitats following hydrological restoration.