Shallow groundwater of unknown quality, mineralisation and recharge processes is a major source of water supply to most households in the informal settlements in the Bonaberi (Douala IV) district, Cameroon. Accordingly, this study (December 2018) investigated the quality, hydrogeochemical controls, and recharge mechanism of 18 shallow groundwater (< 10 m deep) and 6 surface water sources in Bonaberi. Apart from Na+, Cl−, SO42−, Fe, Mn, and Al in some water sources, all other analysed chemical parameters were within the WHO (2011) guidelines for drinking water. The order of major ions abundance (meq/l) in the studied water was Na2+ > Cl− > Ca2+ > HCO3− > SO42 > K+ > NO3− > Mg2+ while the trace element abundance (ppb) was Ti > Fe > Mn > Sr > Ba > Al > Rb > Zn > As > Se > Cr. Two main water types identified in Bonaberi are Na-Cl and mixed Ca-Na-HCO3. Mineral weathering and leaching from pit toilets and waste dumps are major factors influencing groundwater composition. Stable isotopes show overlaps in surface water and groundwater, indicating hydraulic connectivity. The narrow ranges in δ18O values of the shallow groundwater suggest good water mixing and a homogenous aquifer. The major source of groundwater recharge is rainfall occurring by direct diffused rapid recharge through the permeable alluviums. This recharge favours the leaching of pollutants from residential pit toilets into the shallow aquifer. However, the groundwater mixing and its dilution by heavy rains results in relatively low NO3− and Cl− concentrations in the water though relatively higher in densely populated areas. The shallow aquifer in Bonaberi is vulnerable to pollutants generated within the city. Thus, drilling deep boreholes (after detailed hydrogeochemical studies) is recommended for a good quality groundwater supply. This will prevent water-borne infections given the increasing urbanisation.