The aim of this study is to assess the impact of three pharmaceutical substances from the group of antibacterial drugs (ciprofloxacin), estrogens (17α-ethinylestradiol) and cytostatic drugs (5-fluorouracil) on micro-organisms. Enzymatic tests (bioluminescence tests with Vibrio fischeri, dehydrogenase and hydrolytic activity of activated sludge organisms) and growth tests (with Pseudomonas fluorescens and microbial assay for toxic risk assessment with 10 species of bacteria and 1 species of fungi) were performed. The obtained values of concentrations of EC50-t and NOEC showed a different sensitivity of the organisms to the examined active substances. According to the EU criteria, ciprofloxacin was extremely toxic and very toxic to nine species and toxic to three species of bacteria. 17α-ethinylestradiol was extremely toxic and toxic to five species and also harmful to five species. 5-fluorouracil proved to be extremely toxic to seven micro-organisms and very toxic and toxic to five. All active ingredients were non-toxic to activated sludge micro-organisms. The lowest NOEC values for ciprofloxacin and 17α-ethinylestradiol equalled 0.0015 μg/L (V. fischeri), and for 5-fluorouracil 0.08 μg/L (K. gibsonii). The risk assessment, conducted on the basis of the PEC/PNEC quotient, showed a significant risk in relation to micro-organisms caused by the presence of ciprofloxacin and 17α-ethinylestradiol in concentrations detected in surface waters.