Hydrogen (D) and oxygen (18O) stable isotopes in precipitation are useful tools in groundwater recharge and climatological investigations. This study investigated the isotopes in rainfall during the 2013 and 2014 hydrological years in the Douala and Yaounde urban cities. The objectives were to generate local meteoric water lines (LMWLs), define the spatial–temporal variations of the isotopes in rainwater and their relationship to the regional precipitation cycle, and determine the factors controlling the isotopic variation. The LWMLs in Douala and Yaounde were δD = 7.92δ18O + 12.99 and δD = 8.35δ18O + 15.29, respectively. The slopes indicate isotopic equilibrium conditions during rain formation and negligible evaporation effect during rainfall. Precipitation showed similar wide ranges in δ18O values from −5.26 to −0.75 ‰ in Douala and −5.8 to +1.81 ‰ in Yaounde suggesting a common moisture source from the Atlantic Ocean. Enriched weighted mean δ18O (wδ18O) values during the low pre- and post-monsoon showers coincided with low convective activity across the entire region. Enriched isotopic signatures also marked the West African monsoon transition phase during each hydrological year. Abrupt wδ18O depletion after the transition coincided with the monsoon onset in the region. Peak periods of monsoonal rainfall, associated with high convective activities, were characterised by the most depleted wδ18O values. Controls on isotopic variations are the amount effect and moisture recycling. The stable isotope data provide a tool for groundwater recharge studies while the isotopic correlation with regional rainfall cycle demonstrate their use as markers of moisture circulation and detecting climatic changes in precipitation.