In this work, we report on the structural and textural changes in fluvial sediments from Reconquista River´s basin, Argentina, due to processes of contamination with organic matter and remediation by bioleaching. The original uncontaminated matrix showed quartz and phyllosilicates as the main primary mineral constituents and phases of interstratified illite-montmorillonite as secondary minerals. It was found that in contaminated sediments, the presence of organic matter in high concentration causes changes in the specific surface area, particle size distribution, size and distribution of micro and meso, and the morphology of the particles with respect to the uncontaminated sediment. After the bioleaching process, there were even greater changes in these parameters at the level of secondary mineral formation and the appearance of nanoparticles, which were confirmed by SEM. Especially, we found the formation of cementing substances such as gypsum, promoting the formation of macroporous aggregates and the weathering of clay components. Our results indicate that the bioleaching not only decreases the content of metals but also favors the formation of a material with improved characteristics for potential future applications.