Anthropogenic activities in sub-Saharan Africa have increasingly contaminated agro-ecosystems with potentially toxic elements (PTEs), posing risks to food safety and public health. Study assessed the concentration, sources, and dietary health risks of 14 PTEs (As, Pb, Cd, Co, Cr, Hg, Ni, Cu, Fe, Mn, Se, Zn, Th, and V) in a point-source irrigation water (n = 1), agricultural soils (n = 9 composite samples), and commonly consumed vegetables (onion, cabbage, and amaranth; n = 24 composite samples) collected from the Mubuku Irrigation Scheme, western Uganda. Concentrations were determined using inductively coupled plasma–optical emission spectroscopy. Health risks were evaluated using deterministic non-carcinogenic (hazard quotient (HQ) and index (HI)) and carcinogenic (total cancer risk, TCR) assessments, complemented by Monte Carlo simulation (MCS; 10,000 iterations). More than 20% of detected PTEs in vegetables exceeded WHO/FAO limits. Arsenic (2.22–3.57 mg/kg), Pb (2.02–3.66 mg/kg), and Hg (0.42–0.61 mg/kg) consistently exceeded guideline values (0.1, 0.3, and 0.001 mg/kg, respectively), with the highest accumulation observed in amaranth. Irrigation water contained elevated As (1.56 mg/L) and Pb (2.73 mg/L). Estimated HI of PTEs indicated considerable non-carcinogenic risk (HI > 1) for all vegetables, driven primarily by Pb (HQ = 3.21–5.06) and As (HQ = 0.85–2.70) for adults (65–70 kg) and geriatrics (60 kg). Carcinogenic risk estimates (TCR = 5.72×10-⁴–2.99×10-³), including 50th (5.97×10⁻⁴–7.51×10⁻²) and upper-bound (95th) percentile (7.71×10⁻⁴–1.49×10⁻¹) stochastic outcomes, surpassed acceptable thresholds (10⁻⁶–10⁻⁴), indicating probable high lifetime cancer risks, exposure uncertainty and potential risk amplification among high-end consumers. Principal component analysis explained 83.2% of total variance, identifying mixed geogenic and anthropogenic sources, with soils and amaranth as dominant exposure pathways. This study provides the first integrated deterministic–probabilistic–multivariate assessment of PTE risks in a Ugandan irrigation scheme. The findings underscore urgent public health concerns and offer critical baseline evidence to support risk-informed management, targeted remediation, and sustainable agricultural policy interventions.