Inundation associated with flooding and sea level rise is predicted to have major impacts on survival, growth and productivity of mangroves. A manipulative mesocosm experiment was conducted to assess whether nutrient enrichment enhances growth and photosynthesis of waterlogged and salinity stressed seedlings of the mangrove Heritiera littoralis Dryand. Seedlings were fertilized with a three-component granular farm NPK (Nitrogen-Phosphorous-Potassium, 20:20:20) at varied loads under waterlogging with four levels of salinity. Growth was assessed through biomass accumulation, and photosynthesis through photosynthetic quantum yield and leaf Chl content. When seedlings were exposed to both nutrient enrichment and increased salinity, a significant shift of biomass to roots was observed. Seedlings had low value of Chl a/b ratio and photosynthetic distraction resulting in mortality was high in the highest salinity and nutrient levels. These results are useful in explaining failure of regeneration in natural stands of riverine and freshwater bound mangroves following unprecedented flooding events that accrue land based nutrient loads into estuaries and deltas.