Hydrogeochemical processes and flow mechanisms of groundwater in the urban area of Yaoundé were investigated using major chemical constituents, stable isotopes (18O and 2H), and multivariate statistical analysis. Thirty five groundwater samples were collected and analysed for various parameters. Hydrogeochemical evolution visualized with the Gibbs diagram showed that the groundwater is mainly controlled by water–rock interactions. Factor analysis on the other hand identified three major groups of geochemical constituents and showed that weathering and anthropogenic inputs are the dominant factors controlling groundwater chemistry in the study area. Isotopic analyses revealed that oxygen-18 of groundwater (18O = −2.96 ‰ VSMOW) is close to that of rainfall (18O = −2.47), indicating that the groundwater is recharged by rainwater without evaporation. The geogenic composition of urban groundwater in Yaoundé is modified by secondary processes and anthropogenic input.