The responses of the growth rate, motility, and cell shape in the green flagellate Euglena gracilis to different concentrations of waste water substances from the pulp and paper industry were tested in a long‐term study (7 days). Samples before (uncleaned sample) and after (cleaned sample) the treatment in a cleaning system were studied. The influence of different doses of UV‐B radiation on cell shape and motility was also investigated. No statistically significant effects of increasing concentrations of the waste substances both before and after the cleaning process (except inhibition by the undiluted uncleaned effluent) on the growth rate in E. gracilis were observed. Cell shape turned out to be an unreliable physiological parameter for assessing the toxicity at lower concentrations of waste water substances. No significant patterns could be observed in the response of the cell shape to the different concentrations of the waste water substances or to UV‐B radiation. Motility has been concluded to be a more sensitive parameter than cell shape. However, no clear patterns were observed in the response of the motility to the different concentrations of the waste water substances studied. Increasing concentrations of the uncleaned sample demonstrated a defense against UV‐B radiation, due to the high absorbance in the UV‐B range, when effects on motility were examined. We conclude that contrary to the results reported in the literature earlier, cell shape and motility of E. gracilis are not universal physiological parameters for bioassessment at lower concentrations of toxic substances, including metals such as copper and zinc from the pulp and paper industry. The long‐duration tests had, in general, higher significance than those of short duration.