The Water Framework Directive stipulates that water bodies must achieve “good ecological status” in the EU. Although many indicators exist, they are not always able to reveal the subtle effects of low episodic pressure over long exposure times. Itis therefore essential to develop early warning indicators of the surface water quality. For this purpose, the study of phototrophic biofilms seems particularly relevant because of their major role in aquatic ecosystems. The Cleurie river (Vosges, North-eastern France) constitutes an ideal study site for testing the sensitivity ofindicators and their relevance in the WFD context. Due to industrial activities (textiles), this forested headwater stream is exposed to a complex cocktail of molecules characterized by relatively high concentrations of glyphosate (i.e close to environmental quality standards) and aminomethylphosphonic acid (AMPA), its main degradation product but also dyes and optical brighteners. A preliminary study on the watercourse indicates that teratological forms in the diatoms seem to be more abundant downstream of the discharges. The purpose of this study was to determine if the deformities of benthic diatoms would constitute an early and more sensitive marker than the traditional structural indices. In this context, our objective was to estimate in situthe ecotoxic potential of this complex contamination on the diatoms morphology and to identify if these effects can be related to the release of glyphosate and AMPA in the Cleurie river. For this purpose, diatom community structure, presence of deformations and water physicochemistry were monitored on five sampling sites along the river, at seven occasions along the year. In parallel to this field approach, bioassays were performed in 96-well microplates to evaluate the toxicity of glyphosate and AMPA on diatoms under standardized conditions. Short-term (7 days) exposure of the model species Nitzschia paleawas conducted to determine the concentrations of contaminants inhibiting 5, 10 and 50% of their growth (IC5, IC10 and IC50 values). These concentrations and an environmental concentration were then used to expose diatoms under semi-static conditions for 28 days to assess the teratogenic potential of glyphosate and AMPA on diatom morphology. In both experiments, observed deformations were analysed qualitatively (type of deformations) and quantitatively (relative abundance, severity) using morphometric measurements.