Intermittent water supply networks risk microbial and chemical contamination through multiple mechanisms. In particular, in the cities of developing countries, where intrusion through leaky pipes are more prevalent and the sanitation systems coverage is low, contaminated water can be a public health hazard. Although countries using intermittent water supply systems aim to change to continuous water supply systems—for example, Kampala city is targeting to change to continuous water supply by 2025 through an expansion and rehabilitation of the pipe infrastructure—it is unlikely that this transition will happen soon because of rapid urbanisation and economic feasibility challenges. Therefore, water utilities need to find ways to supply safe drinking water using existing systems until gradually changing to a continuous supply system. This study describes solutions for improving water quality in Mukono town in Uganda through a combination of water quality monitoring (e.g., identifying potential intrusion hotspots into the pipeline using field measurements) and interventions (e.g., booster chlorination). In addition to measuring and analyses of multiple chemical and microbial water quality parameters, we used EPANET 2.0 to simulate the water quality dynamics in the transport pipeline to assess the impact of interventions.