The devastating cyclone Aila that hit the south-western coast of Bangladesh on 25 May, all the fresh water bodies of Koyra upazila sadar of southwest region are flooded by tidal surges of rivers channels with sea water intrusion and thus contaminated by all kinds of solid waste and debris as well as salt water inundation. Having no alternative fresh water sources except rain water, forcing this people to use this dirty and polluted water for using their household and other domestic purposes. To find out the necessary present major Biological parameter phytoplankton have been analyzed and compared this analyzed result with surface water quality standard suggested by Bangladesh authority for evaluating the water quality of fresh water ponds of Koyra upazila sadar and to take appropriate initiatives like some management approaches for the betterment of this existing water bodies. The phytoplanktonic abundance of the study area on an average is 82652units/l. The study is catheterized by Cyanophyceae, Chlorophyceae, Bacillariophyceae, Phaeophyceae, Euglenophyceae and Rhodophyceae. From this study the Phytoplankton abundance has found medium to high. But excessive load of some parameters due to addition of domestic waste, agricultural runoff and sea water intrusion by the cyclone Aila, natural quality of water have changed in this study area that caused abnormal phytoplankton growth and algal bloom in some study ponds because of Oscillatoria sp. which is the main sign of Eutrophication.