Magnetic proxy approaches proved to be efficient for potentially toxic elements (PTEs) pollution assessment when targeting forests or areas with a homogenous background where anthropogenic magnetic signals could be easily distinguished. Here, we present a multidisciplinary approach for magnetic susceptibility ( $$x$$x ) and HM assessment in a complex area in the Nile Delta, where geogenic input, land use, and various industries with different fly ash and surface water emissions interfere. Statistical analysis discriminates between the effects of lithologic elements and the concentrations of toxic anthropogenic elements. The studied elements are classified into lithogenic and anthropogenic-related (HMs, Au industry, and fertilizers industry) groups with maximum contamination levels of eight anthropogenic-related and highly toxic PTEs (Cu, Zn, Mo, Cd, Sb, Pb, Hg, and As) in the Akrasha industrial area (pollution load index = 15.84). Considering the whole data set, the numerical correlation of $$x$$x with most PTE concentrations and the pollution load index (PLI) is weak, while it is moderate to strong with lithogenic elements. However, a comparison of lithogenic elements and PTE concentrations along with x-values in two separate clusters supports the correspondence of lithology with elevated x-values in silt and clay-rich soil samples as well as HM concentration in industrial sandy soils. Correspondence between magnetic maps and chemistry data with land use reflects the potential of magnetic proxy methods for qualitative PTE pollution pre-delineation of the polluted spots, provided that lithological conditions are carefully considered.