A study was carried out to investigate the extend of microbiological contaminants associated with sanitary waste in groundwater supplies in a densely populated residential estate. Samples were drawn from sixteen underground wells during wet and dry seasons and assayed for coliform densities in relation to proximity to pit latrines. The wells recorded presence of both total and fecal coliform bacteria, with peak contamination occurring during the wet season (mean total coliform count, cells/100ml – 1268.63) compared to dry season (mean total coliform count, cells/100ml- 520.07). The total coliform count varied significantly between the seasons (t=2.13, p=0.00002, P < 0.05). Similarly there was a significant difference in the fecal coliform count during the seasons (t=2.131, P=0.0064, p< 0.05) with a higher mean count (228.125) occurring during the wet season compared to 14.75 - dry season. A decrease in well depth marked an increase in coliform count during the wet season. Bacterial count was not significantly related to well- pit latrine isolation distance. Presence of E. coli in the groundwater is an indicator of possible presence of harmful pathogenic microorganisms associated with fecal pollution such as Salmonella, campylobacter, Shigella and enteric viruses which cause gastro-intestinal distress. Poorly constructed wells in proximity to pit latrines and open sewers occasioned by small sized landholdings poses a significant health threat to the inhabitants. Hence there is need to create awareness on construction regulatory standards of groundwater wells in order to curb the risk of contracting water-borne infections.