A field experiment was carried out on summer rice (Oryza sativa L) during 2003 and 2004 using different organic mulches – Azolla, rice chaffy grain, saw dust, subabool (Leucaena leucocephala L.) green leaves and FYM under rotational submergence at 5 days after disappearance of ponded water against continuous submergence. The results revealed that rotational submergence reduced the uptake of N, P₂O₅ and K₂O by 40.2, 49.3 and 33.1% respectively as compared to continuous submergence. However, application of organic mulches in rotational submergence improved the uptake of nitrogen (11.1 - 51.9%), phosphorus (12.7% - 67.6%) and potassium (9.3 - 39.1%) compared to without mulching condition. Among the organic mulches,brice chaffy grain recorded maximum uptake of N and K and FYM recorded maximum uptake of P₂O₅. Rotational submergence (cyclic stress) reduced the nutrient availability to the extent of 23.8, 17.2 and 2.0% of N, P2O5 and K2O respectively. Organic mulches under rotational submergence significantly improved the nutrient availability to the extent of nitrogen 33.8 - 59.7%, phosphate 28.2 - 61.8% and potash 1.65 - 9.1% and it was even higher than continuous submergence. Soil water stress reduced the oxidisable soil organic carbon status by 5.13% as compared to continuous submergence, whereas, mulching improved the carbon status by 9.5% to 18.2% and increased the grain yield by 20.5-50.7%. Water supply situation and organic mulches significantly influenced microbial population. Among the mulches saw-dust and FYM increased the microbial population by 37-192% over stress control.