Cypress domes are isolated wetlands dominated by cypress (Taxodium spp.) with multiple subdominant species. Although one of the most common wetlands in the southeastern United States, the number and extent of cypress domes are progressively declining. While tree communities must be resilient to survive both extended periods of flooding and desiccation associated with climate cycles, ongoing changes in land use and climate are altering hydrologic extremes and potentially exceeding the resilience of species. Upland species such as pines and oaks can increase in density in response to persistent shortened hydroperiod, while mature wetland trees including cypress and tupelo can persist for extended periods. This study investigated tree community structure in cypress domes across a gradient of hydroperiods and water depths potentially experienced by cypress domes with altered hydrology. Three decades of water level data were used to describe cypress dome tree community responses to long-term, chronic alterations to hydrology.The tree community structure of cypress dome was correlated with average annual hydroperiod and water depth, but maximum water depth was not significant. Nyssa sylvatica was correlated with extended hydroperiods/deeper water depths, while both Quercus laurifolia and Pinus elliottii correlated with reduced hydrology. The presence of cypress was not correlated with hydrology, presumably because of its dominance in all sample wetlands. Mature (>6 m) wetland trees remained dominant in all sample wetlands with non-wetland trees showing increased abundance when hydroperiods and water depths were below 3 months and 0.075 m, respectively. Sub-adult (<6 m) non-wetland trees became increasingly important when hydroperiods fell below 6 months and were dominant below 3 months. Wetland tree recruitment was reduced when hydroperiods were altered to less than three months and longer than nine months; and average water depths were altered to <0.075 m and>0.225 m. Our study indicates that cypress dome communities may not be as resilient as previously thought. The long-term persistence of cypress domes is not dependent on the ability of mature wetland trees to survive extended periods of flood and drought, but instead maintaining hydrology and recruitment of wetland trees. By utilizing a long-term hydrologic database, a tipping point for cypress domes was observed for water depth and duration of inundation, beyond which the long-term persistence of these systems is in jeopardy.