The present study evaluates how a prolonged artificial flooding regime in impounded mangrove forests influences the regeneration after medium-sized forest destruction created by two hurricanes in 2004 in the Indian River Lagoon, Florida, USA. Disturbance patterns, forest structure, and regeneration were investigated. We found disturbed areas, characterized by uprooted and snapped trees, and intact forests in close proximity. The canopy turnover was greater in forests in higher succession stages with median tree diameter at breast height of 7.6 ± 5.7 cm compared to the intact forest with 3.7 ± 1.2 cm. Larger trees with lower densities were more susceptible to hurricane damage. We observed that regeneration of the open patches was dominated by the flood-tolerant species Rhizophora mangle (89.9%) instead of the faster-growing pioneer species Laguncularia racemosa (7.0%). Some of the disturbed areas created by the hurricanes were not recolonized. The regeneration rate of the disturbed areas expressed by vegetation closure >50% differed between almost zero to 100% in three different impoundments. We concluded that the artificial flooding regime imposed by impoundment is the predominant selective force in the successive process according to the species composition. However, we were not able to detect the driving factors that prevented mangrove establishment in disturbed areas.