Major investments in water supply infrastructure will be required to achieve Sustainable Development Goal (SDG) 6. Safely managed water services are also central to global cholera and diarrhoeal diseases prevention strategies. However, evidence remains scarce on how to efficiently improve piped water services in complex settings where infrastructure investments are most needed. We conducted a process evaluation of a large-scale water supply infrastructure improvement programme in Uvira, Democratic Republic of the Congo, in parallel to a pragmatic trial. Considering three evaluation domains–context, implementation, and population response–, we assessed the validity of the programme’s theory of change and underlying assumptions. Information sources included construction works documentation, operational and billing records from the water utility, and household surveys. The evaluation covers the period 2014–2021. Trial results are not within the scope of this manuscript. The programme did not achieve expected improvements in the water supply service during the evaluation period. Out of 16 assumptions underlying the theory of change, six remained valid, seven partially valid, and three turned out to be invalid. Contextual challenges included extreme flooding in 2020 and the Covid-19 pandemic, which disrupted construction works. Issues related to electricity supply and the rise of Lake Tanganyika emphasise the need for cross-sectoral approaches and consideration of climate change in the planning of water supply infrastructure. Implementation challenges underlined the importance of capacity strengthening alongside infrastructure improvements. Population response elements suggest that affordability and informal practices such as tap sharing should be taken into account. The programme was a good example of early engagement with researchers and provides unique insights into the implementation of large-scale infrastructure improvements in a complex, low-income setting. Pragmatic evaluation approaches should be adopted for the generation of scientific evidence from complex programmes in order to optimise future infrastructure investments contributing to progress towards SDG6.