Aquatic environments in industrialized countries were frequently exposed to numerous pollutants generated by various discharges from municipal, hospital and industrial wastewaters, agricultural! effluents and nonpoint source pollution (Rabodonirina et al., 2015). Aquatic sediments are repositories of this debris and act as sources and sinks for a wide variety of organic and inorganic pollutants (Perelo, 2010). Therefore, even if water quality improves, sediment contamination will remain a 'legacy of the past' (Fórstner etal., 2004). Hydrocarbons may enter the aquatic ecosystem either directly, by effluents or spills, or ¡indirectly by terrestrial runoff or atmospheric deposition. Their persistence in the environment depends mainly on their chemical and physical characteristics (Perelo, 2010). Whereas polycyclic aromatic hydrocarbons (PAHs) are considered to be the most toxic component of oils, recalcitrant aliphatics and other high-molecular weight petroleum hydrocarbons are the primary hydrocarbon fractions found in sediment (Pettigrove and Hoffmann, 2005); although the latter might not be directly toxic to aquatic organisms, they can alter the physical properties of sediments, coat and smother organisms, and contribute to organic enrichment of sediments (Anson et al., 2008). The assessment and management of contaminated sediments is inherently more complex than managing many relatively small and simple contaminated soil and groundwater sites (Reible, 2013). The three main objectives of sediment management strategies are to minimize contaminant risk to human health and the environment, to minimize associated with the remediation technique itself, like habitat destruction and/or modification and to minimize cost (Perelo, 2010). Three sediment management options are currently used, dredging, capping or monitored natural recovery (MNR), and due to the complexity and expensive of sediment remediation process, high technology solutions are not forthcoming. Environmental dredging creates challenges including identification of disposal facilities or the design and construction of confined disposal facilities, controlling resuspension, and minimizing post dredging residual contamination. Installation of sand caps has its own set of challenges. This technology if not designed and placed correctly can cause advective flow that might result in rapid breakthrough of contaminants depending on geo-chemistry and characteristics of the sediments. The monitored natural recovery (MNR) is a remedial approach that relies on natural physical, chemical, and biological processes to reduce ecological and human health risks. MNR is a non-invasive technology which, carefully planned, allows remediation of sediment sites and can result in risk reduction in comparison with dredging and capping. The aim of this work was to evaluate the application of MNR from a freshwater course affected by human activity using sediment biological parameters and next generation sequencing methods (NGS) as potential indicators of biological processes.Centro de Investigación y Desarrollo en Fermentaciones Industriales