This research provides general guidelines for monitoring the environmental quality state of the marine ecosystems using benthic microfauna as a bioindicator tool in the Western Moroccan Mediterranean coastal areas. The current faunistic composition of 18 superficial sediment samples collected in areas having a wild range of environmental conditions have been the subject of factorial correspondence and hierarchical classification analysis, allowing us to follow the distribution patterns of the benthic assemblages. Considering the influence of both hydrodynamic and sedimental conditions on the superficial sediment, recognized in this study as the main environmental factors affecting the distribution of species in this type of environment, we were able to delineate three environmental units, with specific faunistic response related to the corresponding environmental conditions. Leading us to identify the optimal sampling area for the biomonitoring surveys in this region. Shallow and high-energy coastal areas were found to limit data collection and the representation of the sampling area, while low-energy areas were identified as ideal for environmental surveys, showcasing strong faunistic response to stressful conditions. we recommend to conduct the ecological monitoring studies in the 10–30-meter depth range, where the environmental conditions favor the assessment of the current environmental quality state by the benthic microfauna.