Growth inhibition of freshwater microalga Pseudokirchneriella subcapitata caused by a waste water treatment plant (WWTP) effluent extract was investigated using an effect directed analysis (EDA) approach. The objective was to identify compounds responsible for the toxicity by combining state-of-the-art sampling, bioanalytical, fractionation and non-target screening techniques. Three fractionation steps of the whole extract were performed and bioactive fractions were analysed with GC (xGC)-MS and LC-HRMS. In total, 383 compounds were tentatively identified, and their toxicity was characterized using US EPA Ecotox database, open scientific literature or modelled by ECOSAR. Among the top-ranking drivers of toxicity were pesticides and their transformation products, pharmaceuticals (barbiturate derivatives and macrolide antibiotics e.g. azithromycin), industrial compounds or caffeine and its metabolites. Several of the top-ranking pesticides are no longer registered for use in plant protection products or biocides in the Czech Republic (e.g. prometryn, atrazine, acetochlor, resmethrin) and some are approved only for use in biocides (e.g. terbutryn, carbendazim, phenothrin), which indicates that their non-agricultural input into aquatic environment via WWT'Ps should be carefully considered. The study demonstrated a functional strategy of combining biotesting, fractionation and non-target screening techniques in the EDA study focused on the identification of algal growth inhibitors in WWTP effluent.