In Maputo, the capital of Mozambique, nitrate concentrations above 250 mg L−1 in groundwater have been reported. This happens due to the widespread use of latrines and septic tanks that allow for constant infiltration of its content into the soil and eventually to groundwater sources, a situation that is widespread in the Global South and represents a serious threat for human health and for the environment. This is a reflection of limited access to safe and adequate sanitation services, which the local authorities have set to improve in the forthcoming decades with a recently commissioned city-wide sanitation masterplan serving as a basis for the works. In this article, we aimed at understanding whether the infrastructure projected in the masterplan would lead to a reduction of nitrogen reaching groundwater. Currently, according to our calculations, almost 500 tonnes of nitrogen reach the city’s groundwater sources each year, with the masterplan potentially resulting in a 14% reduction, a small reduction due to its reliance on maintaining and expanding fecal sludge services, without considering investments to improve domestic systems (e.g., construction of contained systems). An alternative, not presented in the Masterplan and put forward by the authors, could be the construction of simplified sewers in two of the city’s most densely populated neighborhoods, with a potential 29% reduction in nitrogen reaching groundwater.