The objective of our study was the investigation of the toxic properties of two antimicrobial drugs: oxytetracycline (OTC) and trimethoprim (TMP) in the aquatic environment. The toxic effects were tested according to the OECD guidelines for the testing of chemicals, on the cyanobacteria Anabaena flos-aque, on the alga Pseudokirchneriella subcapitata, on the daphnid Daphnia magna as well as on the activated sludge. We discussed the short term and long term results of tests on cyanobacteria and microalgae. Both experiments were concluded in 72 h allowing direct comparison of sensitivity of the two tested species. The results of our study showed toxic effect in the same range for both groups. In the test on the toxicity of OTC to P. subcapitata we obtained the 72 h ErC₅₀ of 1.04 mg L⁻¹ (72 h ErC₁₀ 0.47 mg L⁻¹) which are lower in comparison to the results on the toxicity to A. flos-aque of ErC₅₀ of 2.7 mg L⁻¹ (72 h ErC₁₀ 1.5 mg L⁻¹). TMP is less toxic to both photosynthetic plankton species. Similar to the test results on OTC, the P. subcapitata is more sensitive to TMP (ErC₅₀ 129 mg L⁻¹; ErC₁₀ 65 mg L⁻¹) than A. flos-aque (72 h ErC₅₀ 253 mg L⁻¹; 72 h ErC₁₀ 26 mg L⁻¹). OTC is toxic to the activated sludge (3 h EC₅₀ 17.9 mg L⁻¹), while the calculated 3 h EC₅₀ value for TMP exceeded solubility for the compound. In comparison to other species, both tested antimicrobials showed low toxicity to daphnids.