The Paraiba do Sul (PSR) and Guandu Rivers (GR) water diversion system (120 km long) is located in the main industrial pole of Brazil and supplies drinking water for 9.4 million people in the metropolitan region of Rio de Janeiro. This study aims to discern the trace metals dynamics in this complex aquatic system. We used a combined approach of geochemical tools such as geochemical partitioning, Zn isotopes signatures, and multivariate statistics. Zinc and Pb concentrations in Suspended Particulate Matter (SPM) and sediments were considerably higher in some sites. The sediment partition of As, Cr, and Cu revealed the residual fraction (F4) as the main fraction for these elements, indicating low mobility. Zinc and Pb were mostly associated with the exchangeable/carbonate (F1) and the reducible (F2) fractions, respectively, implying a higher susceptibility of these elements to being released from sediments. Zinc isotopic compositions of sediments and SPM fell in a binary mixing source process between lithogenic (δ66/64ZnJMC ≈ + 0.30‰) and anthropogenic (δ66/64ZnJMC ≈ + 0.15‰) end members. The lighter δ66/64ZnJMC values accompanied by high Zn concentrations in exchangeable/carbonate fraction (ZnF1) enable the tracking of Zn anthropogenic sources in the studied rivers. Overall, the results indicated that Hg, Pb, and Zn had a dominant anthropogenic origin linked to the industrial activities, while As, Cr, and Cu were mainly associated with lithogenic sources. This work demonstrates how integrating geochemical tools is valuable for assessing geochemical processes and mixing source effects in anthropized river watersheds.