In a context of several directives for transitional and coastal waters masses (Water Framework Directive, Marine Strategy Framework Directive and Bathing Water Directive), the good ecological status of water but also conservation of marine ecosystem should be quickly achieved. The Basque coastline (SE of the Bay of Biscay) is subject to strong human pressures with a high density of population over the year, and especially during the summer with tourist activities. It generates nutrient discharge, water and sediment pollution and impacts the quality of the marine environment. Such pressure and the way to reduce its impacts are the main concerns of authorities Locally, in order to improve wastewater treatment process, an alternative technical solution is applied for one year to reduce bacteriological pollution fluxes. This treatment is based on the injection of a biocidal compound (performic acid) into the outlet pipe before the discharge into the sea. The impact of this new treatment on the environment was considered from chemical and biological aspects on a sedentary benthic population of Mytilus spp settled above the sewage outfall. Samples were collected at different periods of the year between February and August on this location and on an undisturbed reference site located on the artificial intertidal shore. Chemical aspects were apprehended by metal concentrations in biota. Biological aspects were based on physiological status and biometrics indicators. It enables us to look for the phenotypic variations of morphological patterns of the mussel shells in relation to environmental changes. It was completed by an ecological characterisation of the present benthic communities. The communication proposes a detailed description of the method and a presentation of first results which actually does not show any modification of the biological indicators in relation to the new process.