Spatiotemporal variation of human pathogenic bacteria was observed in the surface waters of a monsoonal estuary and these bacteria were also found to be associated with the native fish of two monsoonal estuaries. The temporal variation was in accordance with any monsoonal estuary. Also, the spatial variation in physicochemical parameters and bacterial counts was very evident at any given time. For instance, one sampling location in the estuary consistently had 103 fold higher bacterial counts than the rest of the locations within the same estuary. Coliforms, Salmonella-like (SmLO) organisms, Shigella-like (SLO) organisms, Vibrio parahaemolyticus-like (VPLO) organisms and Vibrio cholerae-like (VCLO) organisms occurred at many locations, but the abundance of each group varied differently with time at different locations in the estuary. Coliforms, unlike others, showed an increase in abundance from post-monsoon to pre-monsoon season. VCLO were the most abundant amongst all. Not all the pathogenic bacteria were widespread throughout the channel indicative of dominance in spatial variation over seasonal in this estuary. Most of the fish samples showed similar trend of bacterial numbers as that in surrounding waters, except a few. Presence of sewage pollution indicator bacteria in the fish indicated that fish served as reservoirs of these bacteria. Thermal death time of randomly picked fish-associated isolates was 30 min at 80 °C and these could survive freezing temperature for 24 h and produce siderophore which can account for their pathogenic nature. The monsoonal estuaries thus render survival ground of such bacteria.