Salmonella is one among the most important biological contaminants in drinking water that possess safety hazards to human life. Faecal contamination of the water, indirectly from the household sewage discharge, municipal sewage etc. attributes to the repeated detection of Salmonella in water. This study aimed to investigate the occurrence of Salmonella and physico- chemical quality evaluation of samples of water collected from food retail outlets of Thrissur and Kollam districts. A total of 50 water samples (25 each from Thrissur and Kollam districts) used for cooking purpose were collected over a period of six months, March to August 2023. Water samples were subjected to comparative evaluation of physico-chemical qualities viz., pH, turbidity, total dissolved solids (TDS) and hardness. Collected water samples were examined for Salmonella spp. by conventional culture method and PCR. Genus specific and virulence genes of the isolates were detected using polymerase chain reaction. The occurrence of Salmonella spp. in samples of water collected from Thrissur was 24 per cent whereas in Kollam district it was only four per cent. The overall occurrence of Salmonella spp. in samples of water collected from both districts was 14 per cent. Physico-chemical parameters of water samples viz., pH, turbidity, total dissolved solids and hardness were within the BIS prescribed standards. The molecular characterisation of Salmonella spp. detected 16S rRNA in all isolates but invA and spvA genes were detected only in 14.28 per cent of the isolates. Hence proper disinfection of water and food sanitation in the retail outlets will help to minimize the risk of foodborne pathogens Keywords: Salmonella, water, physico-chemical quality, food retail outlets