In Sri Lanka, among 2588 Salmonella positive cases, the highest incidences were recorded from Jaffna peninsula during 2005 to 2013. Therefore, the present study aimed to identify the microbiological and chemical contamination status of groundwater (40 well water) sources in Jaffna during November 2016. The total coliform, E. coli, Salmonella spp. and Shigella spp. along with some physico-chemical parameters of groundwater were studied. The results revealed that entire peninsula was contaminated with total coliform and E. coli bacteria and the parameters recorded were not within the WHO and SLS (Sri Lanka Standards) drinking water quality standards. 38% of sampling locations were positive for Salmonella spp. and among them six sampling locations were being used for drinking purposes. The results of the study correlates with the statistics of typhoid cases recorded in Jaffna. Results of the study also revealed that around 80% of wells were not within the values specified in guidelines of the SLS for drinking water quality on electrical conductivity. Further, 15% of wells recorded greater than 10 mgꞏdm–3 nitrate, which is still below the SLS drinking water standards (45 mgꞏdm–3). According to the water quality data, PCA analysis showed that Jaffna town, Nallur, Tellippalai and Kopay DS divisions has similar characteristics for water quality.