Majority of houses in Freetown/Sierra Leone are served by on-site sanitation systems. The faecal sludge from these systems are discharged untreated into the pre-urban environment, posing great risk to water resources and public health. The research investigated the sanitary system of the Kissy Low Cost Housing Estate, examining faecal waste management and it''s effects on drainage water quality and human health. Water samples were collected from various points in the estate, which were analysed for physicochemical and microbiological quality. The sanitary condition of the estate was assessed through observation and discussion with major stakeholders. Two types of toilet systems were found common with one faecal waste official dumping site. Majority of the inhabitants use the bucket toilet system whose content is disposed in dug up holes, gutters, streams, etc contaminating the quality standard of the water. Analysis of the water samples collected showed that most of the parameters monitored fell out side safe limit of WHO guidelines. Findings from this research now revealed that water and sanitation management is crucial and need some external attention.