Increasing environmental pollution is connected with broad applications of dyes and imperfection of dyeing technology. Decolourization of triphenylmethane brilliant green and disazo Evans blue by bacterial and fungal strains and toxicity (phyto- and zootoxicity) of degradation by-products were investigated. Influence of incubation method on dyes removal was evaluated (static, semi-static, shaken). Dead biomass was used for sorption estimation. Toxicity of treated dyes was measured to estimate possible influence on aquatic ecosystems. The zootoxicity test was done with Daphnia magna and phytotoxicity with Lemna minor. Samples were classified according to ACE 89/BE 2/D3 Final Report Commission EC. The best results of removal for all tested strains were reached in shaken samples. In opposite to fungi, bacterial strains decolourized brilliant green more effectively than Evans blue. The most effective bacterial strain was Erwinia spp. (s12) and fungal strains were Polyporus picipes (RWP17) and Pleurotus ostreatus (BWPH and MB). Decolourization of brilliant green was connected with decrease of zootoxicity (D. magna) and phytotoxicity (L. minor). Removal of Evans blue was connected with no changes in zootoxicity and decrease of phytotoxicity in most of samples.