Coastal and marine ecosystems should be sustained by maintaining the better environmental quality for our well-being. The goal of this study was to assess the water quality on the coastlines of Kanyakumari, the southernmost part of Indian mainland. Distribution and abundance of indicator bacteria and opportunistic pathogens related to fecal contamination and antibiotic resistance of the isolates were studied to observe the influence of anthropogenic pressures on coastal waters. Water samples were collected from July’22 to September‘22 from three different ecosystems: Chinnamuttom harbor, Kovalam coast and Manakudy estuary. At each site physio–chemical parameters were noted. Simple main effects analysis showed that the sites have a statistically significant difference in total viable count and total coliform count (p < 0.05). A total of eight indicator bacteria such as E. coli, Klebsiella sp., Enterococcus sp., Aeromonas sp., Proteus mirabilis, Salmonella typhi, Vibrio cholerae and Vibrio paraheamolyticus were identified. Antibiotic sensitivity test by Kirby-Bauer Disk Diffusion method was performed to identify sensitivity pattern of antibiotics. The isolates were exposed to ten antibiotics. All the isolates were resistant to at least one antibiotic, and penicillin was the predominant. Presence of fecal indicators indisputably reveals that the chosen sites are receiving untreated sewage loaded with fecal matter which might have detrimental effect on coastal waters.