Mining activity is often responsible for the drainage of acid or metal-enriched waters to fluvial systems. The release of metals is especially disturbing due to the toxicity and persistence of these products and their accumulation in the biosphere. Hence, a systematic detection and delimitation of highly polluted floodplains and linkages between pollution and high-flow stages would likely assist the improvement of land management and ease the design of mitigation or rehabilitation measures. Here we test how trees growing in different geomorphic positions along a fluvial system uptake metal during floods and how these uptakes can be documented “a posteriori”. To this end, we apply dendrogeochemical analyses to twenty Pinus pinaster Ait. trees growing on the banks of Odiel River (south-western Spain) as well as to five reference trees growing outside the river channel. In the field, trees were sampled with a large-diameter (1 cm) increment borer. In the lab, tree-ring series were dendrochronologically cross dated and separated into 5-yr blocks, so that wood blocks contained the dates of major floods. Then, Inductively Coupled Plasma Mass Spectrometry (ICPM) was employed to evaluate toxic metal concentrations in trees. Results point to clear correlations between the accumulation of toxic metals and the geomorphic position of trees within the fluvial network. We show that morphological units along a river exert control on toxic metal concentrations in trees, with uptake being much higher in trees located on meander cut banks than in trees growing on point-bar structures. Besides, we detect chemical signatures in trees located farthest away from the main river channel after the largest floods, but not in the aftermath of smaller events. We conclude that tree position is the single-most important determinant for metallic pollution in an environment controlled by fluvial processes, but also find that more studies are still needed to determine linkages with individual floods and interactions of metal uptake in roots via the water table in the river corridor.