This study examined the effects of diuron on strains of three major freshwater diatom species, Eolimna minima, Nitzschia palea and Planothidium lanceolatum. These species are frequently recorded in the Morcille river, where diuron runs off during phytosanitary treatments of the vineyards around. Here, there were three diatom exposure groups for each species: 0, 1 and 10µg/L diuron during a fourteen-day laboratory assessment. Diuron water concentration, cell number, photosynthetic activity and gene expression were assessed at 6h, 2, 7 and 14 days after contamination. Diuron exposure altered photosynthetic activity in that the optimal quantum yield of photosystem II (PSII) decreased between 40 and 50% and, for Planothidium lanceolatum at 10µg/L, there was complete inhibition. Genetic responses indicated diuron effects on both photosystem II and mitochondrial metabolism in all three species at both diuron exposure levels. Thus, analysis of the expression of psaA, d1, cox1, nad5 and 12s could be an early biomarker to detect pesticide pollution. Overall, this study revealed differences in diuron sensitivity among the three species: Eolimna minima and Nitzschia palea appeared to be more tolerant than Planothidium lanceolatum. These results suggest that the development of molecular tools, and more precisely of biomarkers, will aid in early assessment of contamination and water quality.