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The physicochemical and textural characteristics of river sediments and, essentially, their clays, are at the center of a network of biological and geochemical factors that are mutually modifying. Therefore, the contamination, the characteristics of the clays, and the associated microorganisms strongly influence each other. In this work, sediments from two sites of the urban Reconquista River, near Buenos Aires City, Argentina, exposed to different environmental contexts were characterized. The huge differences in the organic matter content in the vertical profile between both sediments strongly evidenced the polluted status of San Francisco (SF) site as opposed to the Dique Roggero (DR) site. Thorough physicochemical and textural characterization of the sediments and their clay fraction performed by pH, Oxidation-reduction potential (ORP), spectrophotometry, XRD, laser diffraction, N2 adsorption–desorption isotherms, EDS, and SEM measurements revealed that organic matter (DR: 41 ± 5 g kg−1; SF: 150 ± 30 g kg−1) intervened in the retention of heavy metals (DR: 5.6 mg kg−1 Zn, 7 mg kg−1 Cu, 3.1 kg−1 Cr; SF: 240 mg kg−1 Zn, 60 mg kg−1 Cu, 270 mg kg−1 Cr) and affected the level of association and the formation of mineral–organic aggregates (DR: 15 ± 3 μm; SF: 23 ± 4 μm). This can be decisive in the surface interaction required for the establishment of bacterial assemblages, which determine the biogeochemical processes occurring in sediments and have a key role in the fate of contaminants in situ and in the remediation processes that need to be applied to restore the anoxic contaminated sediments. [ABSTRACT FROM AUTHOR]