Although water regime modification and salinity are recognised as significant threats to wetland ecosystems worldwide, the effects of long-term saline flooding (decades) on woody tree persistence are poorly quantified. We compared the condition, growth, structure and reproduction (sexual and asexual) of mature individuals of the clonal tree, Melaleuca ericifolia (Myrtaceae), that experienced continual ([30 years) flooding with trees that were only intermittently (approximately every 5 years) flooded. An index developed to assess the condition of multistemmed trees found that continually flooded trees were in significantly poorer condition than intermittently flooded trees, having lower crown cover, foliar cover and foliar density, and a higher incidence of dead stags and dieback. Annual stem growth correlated strongly with condition scores. Evidence for a tradeoff between sexual and asexual reproductions was found; flooded trees were constrained in their vegetative lateral spread (\12 m dia.) and flowered more than intermittently flooded trees, which were not restricted in lateral spread (*30 m dia.). Flooded trees used intensively by the colonially roosting Australian Sacred Ibis (Threskiornis molucca) were in especially poor condition. These trees flowered infrequently and produced the lowest number of infructescences, but produced many new vegetative stems (ramets) within their centre. Although chronic flooding appeared to compromise the condition of M. ericifolia trees in Dowd Morass, their existence upon woody hummocks (*40 cm high) upon which they are able to produce new stems is likely to be a key mechanism in their persistence. It is unknown, however, how long this process can maintain the existing population. Production and maintenance of a large aerial seed bank by living mature trees under flooded conditions may allow M. ericifolia to regenerate sexually upon drawdown and may be important for population persistence in the longer term.