This study assesses the water resources and environmental challenges of Lagos mega city, Nigeria, in the context of climate change. Being a commercial hub, the Lagos population has grown rapidly causing an insurmountable water and environmental crisis. In this study, a combined field observation, sample analysis, and interviews were used to assess water challenges. Observed climate, general circulation model (GCM) projections and groundwater data were used to assess water challenges due to climate change. The study revealed that unavailability of sufficient water supply provision in Lagos has compelled the overwhelming population to depend on groundwater, which eventually caused groundwater overdraft. Salt water intrusion and subsidence has occurred due to groundwater overexploitation. High concentrations of heavy metals were observed in wells around a landfill. Climate projections showed a decrease in rainfall of up to 140 mm and an increase in temperature of up to 8 °C. Groundwater storage was projected to decrease after the mid-century due to climate change. Sea level rise would continue till the end of the century. As the water and environmental challenges of Lagos are broad and the changing characteristics of the climate are supposed to intensify them as projected, tackling these challenges requires a holistic approach from an integrated water resources management perspective.