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Flooding imposes severe selection pressure on plants, principally because excess water in their surroundings deprives the plants from certain basic resources such as oxygen, carbon dioxide and light for photosynthesis. Here, the effects of nitrogen and phosphorus application and their application time, on four Indica rice cultivars and their tolerance to submergence under turbid and clear flood water was studied. Submergence tolerance on metabolic changes, photosynthetic (Pn) rate and ethylene accumulation were evaluated. Submergence substantially reduced survival, chlorophyll, soluble sugars, Pn rate across cultivars with drastic reduction in IR-20. Sub1 cultivars showed greater Pn rate as compared to sensitive cultivar under submergence because of better protection of chlorophyll, more stomatal conductance leading to higher survival. Turbid water resulted in lower under-water photosynthesis because of poor light transmission, chlorophyll retention and silt deposition and ultimately poor survival. Foliar spray of N after desubmergence along with basal P improved the chlorophyll, soluble sugars and Pn rate and extenuated ethylene accumulation and shoot elongation resulting in significantly higher survival. To the best of our knowledge, this is the first time that such a study has been performed. Crop establishment could therefore be enhanced in areas where untimely flooding is anticipated by applying basal P and foliar spray of post-submergence N.