The contamination of water resource and food chain by persistent organic pollutants (POPs) constitutes a major environmental and human health concern worldwide. The aim of this study was to investigate the levels of POPs in irrigation water, soil and in Amaranthus viridis (A. viridis) from different gardening sites in Kinshasa to evaluate the potential environmental and human health risks. A survey study for the use of pesticides and fertilizers was carried out with 740 market gardeners. The levels of POPs (including organochlorine pesticides (OCPs), polychlorinated biphenyls (PCBs), polybrominated diphenyl ethers (PBDEs), and polycyclic aromatic hydrocarbons (PAHs)) were analyzed in irrigation water and 144 vegetable samples collected from different gardening sites. The assessment of potential human health risk was estimated by calculating daily intake and toxic equivalency to quantify the carcinogenicity. The results show highest PAH levels in A. viridis from all studied sites. The concentrations of the sum of seven PCBs (Σ7PCBS) congeners in analyzed plants ranged between 15.89 and 401.36 ng g−1. The distributions of OCPs in both water and A. viridis were congener specific, chlorpyrifos-ethyl and p,p′-DDE were predominantly detected. Among PBDEs, only BDE47 was quantified with noticeable concentration in A. viridis, while no PBDEs were detected in irrigation water. Higher estimated daily intake values indicate that consuming leafy vegetables might associate with increased human health risks. However, calculated incremental lifetime cancer risk values indicates no potential carcinogenic risk for the local population. The results of this study provide important information on A. viridis contamination by POPs and strongly recommend implementing the appropriate measures to control the use of chemicals used in studied gardening areas. Thus in Kinshasa, urban agriculture control programs for POPs and fertilizers is very important in order to protect the public health through direct and dietary exposure pathways.