The green flagellate Euglena gracilis has been used as a model organism to elucidate the possible large-scale and short-term effects of waste substances from the pulp and paper industry on photosynthetic efficiency (PE). Different concentrations of waste substances before and after treatment in a cleaning system were studied. The uncleaned sample at concentrations up to 1:10 and the cleaned sample at concentrations up to 1:5 showed stimulating effects on the PE after 7 days of incubation compared to the control. The effects of waste substances on the PE of E. gracilis were also studied in combination with short-term studies (20 and 40 min) of ultraviolet-B radiation (UV-B, 280–320 nm). It was shown that increasing concentrations of the uncleaned sample had continuously stimulating effects on the PE and worked protectively against UV-B radiation. The cleaned sample exhibited no effects, or negative effects, on the PE of E. gracilis together with UV-B radiation compared to the experiments with only UV-B radiation. At the concentration 1:1 of the cleaned sample an increase in the PE was detected due to the high concentration of the coloured substances and a decrease in the UV-B penetration. PE revealed itself to be highly sensitive for detecting toxic effects on E. gracilis and is thus very promising for use in regular toxicity tests of waste water from pulp and paper industry.