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As the human population grows and more areas in the world urbanise and industrialise, certain contaminants, such as heavy metals (HMs), are increasing uncontrollably in our water bodies, which poses public health risks. Contributing to ensuring access to portable water and public health protection, this study assessed the levels, spatial distribution and sources of HMs in water resources of the Keta Wetland Complex (KWC) Ramsar Site. Groundwater (GW) and surface water (SW) samples from 80 different locations in the study area were analysed for 16 HMs – Al, As, Cu, Cd, Co, Cr, Cu, Fe, Hg, Mn, Ni, Pb, Sn, Ti, V, Zn, alongside physicochemical and major ions. Results from descriptive statistics comparable to World Health Organisation (WHO) benchmarks showed that all heavy metal levels were within acceptable ranges. The Ficklin-Caboi diagram inferred relatively low dissolution of the HMs. However, Hazard Quotient (HQ) and Lifetime Cancer Risk (LCR) assessments revealed the non-carcinogenic and carcinogenic impact of arsenic on both children and adult populations in some samples, especially at Adina, Akatsi, Anyanui, Keta, and areas around the Avu lagoons. The combined toxicity assessment for all investigated metals exceeded 1 for 50% of GW and 49% of SW for adults, and 75% of GW and 61% of SW for children. Based on the association between the HMs and physicochemical variables, natural and anthropogenic sources of the HMs, namely mineral weathering, agricultural runoff from fertiliser and manure application, effluents from sewage and human waste, were identified. It is therefore deduced that the continuous consumption of GW and SW in the area can pose chronic effects on human health. The findings hence point to the need for management strategies to safeguard the quality of water sources in the KWC.