The investigation was carried out to examine the health hazard indicating bacteria along with some physical and chemical parameters of water and sediment of the Karnafully river including estuarine area from three stations for four months during March - April and June - July in pre-monsoon and monsoon periods. The Total Bacterial counts (TBC) were detected and analyzed the health hazard bacteria such as Escherchia coli, Streptococci sp. and Staphylococcus, Salmonella and Vibrio cholerae. Salmonella and Vibrio cholerae were recorded irregularly in different months in three sampling stations.Total bacterial population always higher in the sediment than water of Karnafuly river estuary. Health hazard bacteria were indicating positive correlation with water temperature and negatively correlated with salinity, pH and as well as Dissolved oxygen. The water parameters and occurrence of health hazard bacteria indicated that water and sediment were polluted and unhygienic for drinking and even washing without treatment.