In this study, we applied the SOM for ecological assessment using benthic macroinvertebrates in aquatic ecosystem. First, Chapter I, SOM was utilized to extract information from complex data of environmental variables and benthic macroinvertebrate communities residing in different micro-habitats. Although the sampling was carried out in a limited area, the patterns of environmental variables revealed spatial heterogeneity. The clustering of benthic macroinvertebrate communities in the trained SOM was efficient in showing temporal variation and evaluating water quality according to the conditions of different micro-habitats. Consequently, local spatial heterogeneity is important in revealing dynamics of community abundance and biotic indices, especially regarding restoration processes in polluted streams. Chapter II, the samples were grouped into three main clusters corresponding to distinc EPTC assemblages in the tributary streams of the Garonne River catchment, southern France. Lower richness and diversity of macroinvertebrates were observed in the areas affected by agricultural land use, being associated with high Total Dissolved Solids (TDS), Nitrate (NO3) and Chemical Oxygen Demand (COD). Tolerant EPTC species were identified as controlling parameters for the changes in the assemblages collected at the agricultural-impacted sites...