Present study is the first ever investigation on water quality based on pathogenic bacterial abundance in the Rushikulya estuary, east coast of India. Analysis of water and sediment samples collected from the Rushikulya estuary during monsoon and post-monsoon indicates seasonal variability along with dominance of pathogenic bacteria in sediment as compared to water. Further, higher abundance of pathogenic bacteria during monsoon suggests the significant role of monsoonal discharge. The study reveals a close association between water quality parameters like (BOD, SiO4 and PO4) and abundance of pathogenic bacteria (Total Streptococcus, Fecal Coliform). Meanwhile abundance of E. coli, FC and SHLO, both in water and sediment, were found maximum in Rushikulya estuary when compared to other estuarine ecosystems of India. Considering Rushikulya estuarine environment as one of the world-famous Olive Ridley turtle nesting habitats, deterioration of water quality associated with pathogenic bacterial abundance is a major concern and needs immediate attention.