Deformities in diatoms are increasingly used as an indicator of toxic stress in freshwaters. However, the percentage of deformities alone often fails at highlighting the magnitude of toxic exposure. It has been suggested that the severity of the deformation (degree of departure from normal form) could be a valuable aspect to consider in addition to the percentage of deformities in an assemblage. An approach combining the assessment of deformities coupled with information on their severity could improve the sensitivity of this biomarker. With the aim of quantifying the deviation from the normal form, we tested the applicability of geometric morphometry to evaluate the degree of deformities in different diatom species. We used photomicrographs of deformed specimens from laboratory cultures of Gomphonema gracile and of Achnanthidium minutissimum from field samples collected along a gradient of toxic contamination. The geometric morphometry approach is based on several landmarks positioned on the outline of the diatom valves, followed by a Procrustes superimposition analysis to determine shape variations. Statistical analyses were conducted based on the geometrical coordinates of the landmarks. The geometric morphometry approach revealed a gradient in the intensity of the deformities observed on G. gracile and A. minutissimum, in-line with a priori, visually-determined (subjective) classifications. A relationship between the degree of deformity in A. minutissimum and a gradient of zinc contamination was found. Geometric morphometry provided encouraging results to objectively quantify the intensity of diatom deformities affecting valve outline, and could easily be implemented in further automatic diatom identification developments.