By 2010 Africa's urban population will have grown to over 420 million with on-site sanitation the predominant excreta disposal option. The use of on-site sanitation has important public health benefits but can result in large faecally derived loadings of nitrogen and chloride to groundwater resources. Nitrate is of particular concern, with elevated concentrations linked to potentially serious health problems. N and Cl can derive from natural sources so it is important to quantify the additional impact of human activities. Several authors have used empirical relationships between nitrate and chloride concentrations to assess the extent to which excreta influences groundwater quality. However, these relationships have assumed fixed loadings from excreta. Relationships between N and Cl have been extended here by adding country-specific estimates of average annual per capita nitrogen and chloride content of, and loading from, excreta. The results are compared with groundwater monitoring results from two very different mid-sized African cities (Timbuktu, Mali and Lichinga, Mozambique) where the vast majority of residents use on-site sanitation and are dependent on the subsurface water for drinking purposes. The results illustrate the impact of urbanisation on groundwater quality. They are compared with data from other African cities to allow the calculation of a general nitrate and chloride relationship for unsewered African urban areas. Potential interventions to help arrest rising nitrate levels and so provide a public health benefit are also examined.