Background: Pit latrines are the most common human excreta and urine disposal facilities in low-income countries because they are economical. However, leachate from the facilities may percolate into the ground and compromise groundwater, necessitating periodic monitoring of nearby groundwater. This study assessed the effects of pit latrines on borehole and well water in Adesoye, Barracks, Onigbongbo, Arowojobe, and Shonibare in Maryland, Lagos, Nigeria. Methods: Water samples were analysed for physicochemical parameters (electrical conductivity, total dissolved solids, hardness, calcium, pH, and chloride), heavy metals (lead, nickel, cadmium, copper, and zinc) and microbial content (bacteria, coliforms, and fungi). The mean values of each parameter was compared with the World Health Organization standards and used to calculate the average daily intake (ADI) and hazard quotient (HQ) of the heavy metals. Results: The physicochemical analysis revealed that each of the borehole and well water samples contained permissible levels of electrical conductivity and calcium. They also contained one or more non-permissible levels of pH, hardness, total dissolved solids, and chloride. The heavy metal analysis revealed non-permissible levels of lead and nickel in all of the water samples, while other heavy metals were within the permissible limits. Total bacteria and coliforms were above the permissible limits in all of the water samples, while fungi were undetected in some samples. The ADI and HQ of the heavy metals were within the threshold limit. Conclusion: The results suggest that groundwater in the areas is unsuitable for consumption. Consumers should treat groundwater and seek experts’ advice before sinking groundwater.