Samples of water and sediment were collected from July to December 2009 in Kottaipattinam coast (Palk Strait, Southeast coast of India). Kottaipattinam coast is one of the major fish landing centre in Palk Strait and receives a considerable amount of sewage and man made waste. Qualitative and quantitative analysis of the composition of the microbial flora were conducted on samples from three stations. The highest bacterial densities, in water and in sediment samples, were found in December and the lowest, in August. Among Gram-negative bacteria, the predominant genus was Pseudomonas; Aeromonas, Vibrio and Flavobacterium were also recorded. Gram-positive bacilli were abundant at all sampling points. Along with physico-chemical parameters were also monitored at every month of sampling.