The accumulation of trace metals in the environmental compartments of coastal rivers is a global and complex environmental issue, requiring multiple tools to constrain the various anthropogenic sources and biogeochemical processes affecting the water quality of these environments. The Valao fluvio-estuarine system (Rio de Janeiro, Brazil) presents a challenging case of a coastal river contaminated by both modern and historical anthropogenic metal sources, located in the land and in the intra-estuary, continuously mixed by tidal cycles. This study employed a combination of spatial distribution analysis of trace metals including gadolinium (Gd), zinc (Zn) isotopic analyses, and X-ray absorption spectroscopy (XAS) to distinguish between these sources. The concentrations of metals in both dissolved (water samples) and surficial sediment compartments (Suspended Particulate Matter and sediment samples) display an overall enrichment trend from upstream to downstream. Multivariate statistical analysis allows to discriminate geogenic elements derived from watershed geology (Ti, K, and Mg) vs anthropogenic contaminants from urban runoff and domestic sewage discharges (Cu, Cr, Pb, Zn, and Gd); and legacy metal contaminants (Zn and Cd) remobilized from ancient metallurgical wastes and transported upstream in the estuary during tidal cycles. The anthropogenic Gd concentration in the dissolved compartment increases along the watercourse, highlighting continuous ongoing sewage discharge. Zinc solid speciation also indicates that Zn contribution from legacy metallurgy waste is primarily associated with sulfide-Zn and Zn-phyllosilicate in the outlet estuary, while in upstream sediments of fluvio-estuarine system, Zn is found bound to organic matter. Zinc isotope systematically reveals a progressive downstream shift to heavier isotope compositions. Upstream, the relatively pristine site and the urbanized section of the river exhibit a relatively uniform δ66/64Zn value (+0.20 ± 0.07 ‰) in suspended particulate matter (SPM) and surficial sediments. These results indicate that domestic sewage discharges contribute to Zn enrichment in sediments of the Valao fluvio-estuarine system but without modifying its isotope signature in sediments. The sediment of the downstream estuarine section shows a heavier δ66/64Zn value (+0.48 ± 0.08 ‰), indicating the strong influence of the intra-estuarine source identified as the historical metallurgic contamination. An integrated view of the geochemical tracers allows thus inferring that the untreated sewage and legacy metallurgical contamination are the primary sources of anthropogenic Zn contamination. It highlights the progressive mixing along the estuarine gradient under tidal dynamics. The influence of the former source continuously expands from the headland towards the estuary.