Highlights • Predominant drivers of the unregulated shallow aquifer degradation in Cotonou were analysed using major ions, Cl/Br molar ratios and stables isotopes as environmental tracers. Vulnerability of this unofficial groundwater resource is due to either salinization or sewage leakage, which is temporally and spatially variable. • Increasing risks from sewage and septic tank leakage during the wet season in neighbourhoods located in discharge areas compared with increasing risk during the dry season in the recharge area. • Mixing with pond water and saline Lake Nokoué water highlight increased risks of shallow groundwater salinization during the dry and small wet seasons in discharge areas. Abstract In Cotonou, as in many expanding West African cities, major population growth and infrastructural development has not kept up with informal settlement development onto floodable plains and marshes. The population of the slum, which makes up about 60% of the city's inhabitants, is highly disadvantaged and vulnerable to rising sea levels, flooding, sanitation and waste management issues. However, the risks associated with the use of contaminated shallow groundwater for domestic purposes are less recognised. Our study demonstrates that, in many instances, the cheaper option of the use of shallow groundwater from the coastal Quaternary aquifer for domestic purposes represents a significant risk for the poorer residents of Cotonou through the voluntary (drinking) or non-volontary (dish washing, cooking) consumption of this unmonitored and untreated water resource. In the 3 neighbourhoods surveyed, environmental tracers (major ions, Cl/Br molar ratios and stables isotopes) showed that this shallow aquifer is degraded by seawater intrusion as well as septic and sewerage contamination. In particular, the higher NOx concentrations correspond to ranges associated with sewerage and septic tank effluent pollution and the major ion concentrations and delta H-2-delta O-18 signatures showed that high salinity values are where groundwater mixes with saline Lake Nokoue water. The population using this resource from local wells should be made aware of seasonal changes in groundwater contamination and potential health risks associated with sewerage and septic tank contamination.