Exposomics is assessment of organism exposure to high priority environmental pollutants in an ecosystem using OMIC technologies. A virtual organism (VO) is an artificial property-tool (OMIC) reflecting exposomic process in compartments of real organisms. The exposomics of aquatic organisms inhabiting Lake Victoria (L.V.) and Three Gorges Reservoir (TGR) were compared using VOs. The two reservoirs are heavily depended on for food and water both in Africa and China. The target priority pollutants in the reservoirs were polyclic aromatic hydrocarbons (PAHs) and persistent organic pollutants such as polychlorinated biphenyls (PCBs), organochlorine pesticides (OCPs), medium chain chlorinated paraffins (MCCPs) and short chain chlorinated paraffins (SCCPs). The VOs showed that in a period of 28 days, aquatic organisms in TGR were exposed to total (∑) PAHs of 8.71 × 10−6 mg/L, PCBs of 2.81 × 10−6 mg/L, OCPs of 2.80 × 10−6 mg/L, MCCPs of 8.9 × 10−10 mg/L and SCCPs of 1.13 × 10−7 mg/L. While in a period of 48 days, organisms in L. V. were exposed to total (∑) PAHs of 7.45 × 10−6 mg/L, PCBs of 4.70 × 10−6 mg/L, OCPs of 3.39 × 10−8 mg/L, MCCPs of 4.6 × 10−10 mg/L and SCCPs of 3.6 × 10−9 mg/L. The exposomic levels in TGR after 28 days were higher than those in Lake Victoria after 48 days. In both reservoirs, bioaccumulation levels are above set standards for aquatic organisms. The sources of the pollutants into the reservoirs were diagnostically determined to originate from anthropogenic processes such as petrogenic, diesel emissions, biomass burning, coal combustion, electronic wastes, traffic emissions and historic uses.