Glyphosate is the active ingredient in a range of widely used herbicides. The aim of this work is to evaluate the effects of two commercial herbicides, Roundup and Avans, on the motility, velocity, and gravitactic orientation of the aquatic flagellate Euglena gracilis. An early warning system, called ECOTOX, has been used for monitoring the different parameters of movement. The motility was not affected by Roundup and Avans after short period tests (0, 30, and 60 s). However, gravitactic orientation of the cells was affected at concentrations of 1.25 g l−1 and above when treated with Avans, whereas treatments with Roundup showed no specific changes after short period tests. Velocity of the cells was affected by both herbicides, but the effects of Avans were shown to occur at lower concentrations in comparison to Roundup. Avans showed lower no observable effect concentration (NOEC) values in comparison to Roundup for the different parameters after short period tests. After long period (7 days) tests, NOEC values were similar except for the upward swimming, where Avans had a NOEC value of 100 μg l−1 and Roundup 200 μg l−1. The results demonstrate that Avans containing trimethylsulfonium salt of glyphosate is more toxic to E. gracilis than Roundup, which contained isopropylamine salt of glyphosate.