Nutrient like ammonia, nitrite, nitrate and inorganic phosphate and some hydrographic parameters were estimated for one year from two distinct mangrove ecosystems of Cochin backwaters viz. Puduvypeen and Nettoor. The ammonia values showed higher concentrations at Puduvypeen as well as at Nettoor and the annual average for the different stations ranged from 13.13 to 37.84 mu mol/l and 64.44 to 70.78 mu mol/l respectively. Seasonal variation was well marked during monsoon at Puduvypeen whereas at Nettoor it was during premonsoon. The annual averages for Nitrite, Nitrate and Phosphate ranged from 0.74 to 1.87 mu mol/l, 2.72 to 7.41 mu mol/l and 14.79 to 30.61 mu mol/l respectively at Puduvypeen whereas at Nettoor it ranged from 4.04-4.75 mu mol/l, 10.09-14.53 mu mol/l and 18.97-20.22 mu mol/l respectively. The annual ranges of Temperature and pH were 26.50 to 35.0 degrees C and 6.46 to 8.64 respectively. The salinity varied from almost freshwater to sea water conditions. The dissolved oxygen values ranged between 2.00 and 8.75 ml/l