This study was conducted to assess the bacteriological quality of alternative drinking water supply options in southwest coastal areas of Bangladesh. A total of 90 water samples were collected during both dry and wet seasons from household based rainwater harvesting systems (RWHSs), community based rain water harvesting systems (CRWHSs), pond-sand filters (PSFs) and ponds. The samples were evaluated for faecal coliform, Escherichia coli and Heterotrophic Plate Count, as well as Vibrio cholerae, Salmonella spp., Shigella spp. and Pseudomonas spp. Physico-chemical parameters (pH, electrical conductivity, and color) were also examined. In addition, sanitary inspections were conducted to identify faecal contamination sources. All options showed varying degrees of indicator bacterial contamination. The median E. coli concentrations measured for RWHSs, CRWHSs, PSFs, and ponds were 16, 7, 11, and 488 cfu/100 ml during the wet season, respectively. Vibrio cholerae O1/O139, Salmonella and Shigella spp. were not found in any samples. However, Vibrio cholerae Non-O1/Non-O139 and Pseudomonas spp. were isolated from 74.4% and 91.1% of the water samples collected during the wet season. A maximum pH of 10.4 was found in CRWHSs. Estimation of the disease burden for all options in disability adjusted life years (DALYs) showed an increased disease burden during the wet season. According to sanitary inspections, poor maintenance and unprotected ponds were responsible for rainwater and PSF water contamination, respectively. The findings of the present study suggest that alternative drinking water supply options available in southwest coastal Bangladesh pose a substantial risk to public health.