A range of pathogens, including total and faecal coliforms, was monitored in the Kampala city water supply. The results show that water samples drawn from just-treated water prior to its distribution to the supply occasionally contained above allowed levels of pathogen counts. Water samples at consumer points along the supply line contained fluctuations of total and faecal coliform counts with significant high counts during rainy season. Owing to sprawling human settlements and various urban construction and industrialization, interference with the natural drainage system is increasingly creating effluents significant pathogen and other pollutants into the water system, with concomitant implications on the efficacy of their removal from the city drinking water supply. Pathogen levels and the by-products of chlorinating water and associated health implications are discussed in light of public health, cost effectiveness and sustainability. Optimal levels of chlorine in water supply line and low faecal coliform bacteria concentration are important criteria for protecting water quality.