Soil contamination by heavy metals is a significant environmental challenge impacting agricultural production, food safety, and ecosystem sustainability. This study seeks to identify and characterise the concentration and spatial distribution of heavy metals in agricultural soils across several industrially affected regions in Albania, as well as to evaluate their transfer to agricultural products and their ramifications for human health and soil quality. The research technique encompassed the systematic sampling and monitoring of soils at depths of 0–30 cm, 30–60 cm, and 60–90 cm, in addition to the analysis of agricultural products from polluted locations. Laboratory investigations aimed to ascertain the amounts of chromium (Cr), nickel (Ni), cobalt (Co), copper (Cu), lead (Pb), mercury (Hg), and arsenic (As), compared to European Union (EU) soil quality requirements. Supplementary evaluations encompassed marine goods in regions with verified industrial contamination. The findings demonstrate that heavy metal levels at the former Elbasan Metallurgical Complex substantially surpass EU legal thresholds. Chromium contents vary from 1041 to 1090 mg/kg, whereas nickel averages 473 mg/kg—significantly exceeding acceptable limits. Increased concentrations of mercury were identified in soils, marine waterways, and human biomarkers next to the defunct PVC facility in Vlora. Analogously, elevated levels of arsenic and lead were detected in regions next to historic nitrogen fertiliser and battery production sites. A robust positive association was identified between metal concentrations in agricultural crops, validating the bio-transfer along the food chain. The study indicates that prompt remedial efforts are necessary, encompassing the application of biological (phytoremediation), chemical, and physical treatment methods. It is advisable to use tolerant plant species and implement adaptive cultivation practices to rehabilitate contaminated soils and improve agricultural and environmental resilience.