Urban and peri-urban farmers in Malawi increasingly use treated and untreated wastewater for vegetable production, but little is known about the extent of heavy metal accumulation in both exotic and indigenous vegetables, particularly with respect to differences between edible tissues (leaves vs. stems). This study addresses this gap by measuring the concentrations of cadmium (Cd), chromium (Cr), lead (Pb), zinc (Zn), and copper (Cu) in wastewater, soils, and six vegetables including three exotic and three indigenous irrigated with effluent from the Soche Wastewater Treatment Plant in Blantyre. Metal concentrations were determined using Atomic Absorption Spectrophotometry. Wastewater contained Zn (0.01 ± 0.001 mg/L) and Cu (0.02 ± 0.018 mg/L), both below World Health Organization (WHO) and Malawi Bureau of Standards (MBS) limits (Zn: 0.2 mg/L; Cu: 2 mg/L), while Cd, Cr, and Pb were below detection limit. In soils, Zn reached 56.4 ± 0.5 mg/kg, exceeding the WHO limit of 36 mg/kg; other metals remained within WHO permissible values. Vegetables showed species- and tissue-specific variation in metal accumulation: Cr reached 4.65 mg/kg in
Cucurbita moschata stems, Cd up to 0.31 mg/kg in
Amaranthus retro-flexus leaves, and Pb up to 4.09 mg/kg in
Brassica rapa stems—all above FAO/WHO permissible limits (2.3, 0.2, and 0.3 mg/kg, respectively). Duncan’s post hoc analysis confirmed significant differences (
p < 0.05) across matrices and plant parts, with leaves generally accumulating more Zn and Cu than stems. Principal component analysis (PCA) revealed that Zn, Cu, Cr, and Pb in the wastewater-soil-vegetable system largely share a common source, likely wastewater effluent and historical soil contamination, while Cd showed a more sporadic distribution, highlighting differential accumulation pathways. Health risk assessments revealed high Health Risk Index (HRI) values, with
Brassica rapa stems (HRI = 92.3) and
Brassica rapa subsp.
chinensis leaves (HRI = 82.2) exceeding the safe threshold (HRI > 1), indicating potential chronic risks. This study reveals potential health risks associated with wastewater irrigation due to heavy metal accumulation in edible vegetables, and therefore recommends further research on metal speciation, seasonal variation, and bioaccumulation at different crop growth stages.
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