Flooding and salinity fluctuations are common in mangrove systems. Sometimes these events are long-lasting, persisting several months. With an increased frequency of heavy rainfalls and terrestrial run-off, subsequent floods have been associated with massive mangrove mortality and failure to regenerate in the region. Owing to climate change, these events are expected to be more common in the future. We investigated how three weeks of submergence in water of different salinities affected the photosynthetic rates in seedlings of three common mangroves: Bruguiera gymnorrhiza (L.) Lamk.; Avicennia marina (Forssk.) Vierh.; and Heritiera littoralis Dryand. We found that photosynthesis and survival rates declined with increasing salinity and submergence time for all species. Prolonged submergence caused a significant decline in photosynthetic rates (as electron transport rate – ETR) for B. gymnorrhiza (P = 0.021) and H. littoralis (P = 0.002), whereas significant effects of both salinity (P = 0.003) and submergence (P = 0.023) were observed between species. Maximum diurnal values of ETR declined in the order of A. marina > B. gymnorrhiza > H. littoralis. After submergence, survived seedlings were tended normally, watered twice a day with freshwater. Three seedlings of B. gymnorrhiza from freshwater and 33% seawater treatments and of A. marina from freshwater treatment displayed signs of recovery for the first 3–5 days, but after that they died. We conclude that submergence time and water salinity will affect the performance of mangrove areas, such that areas experiencing prolonged submergence with flooding dominated by saline water might be most severely impacted.