Phytoplankton constitute an important component of surface water ecosystems; however little is known about their contribution to biotransformation of organic micropollutants. To elucidate biotransformation processes, batch experiments with two cyanobacterial species (Microcystis aeruginosa and Synechococcus sp.) and one green algal species (Chlamydomonas reinhardtii) were conducted. Twenty-four micropollutants were studied, including 15 fungicides and 9 pharmaceuticals. Online solid phase extraction (SPE) coupled with liquid chromatography (LC)-high resolution tandem mass spectrometry (HRMS/MS) was used together with suspect and nontarget screening to identify transformation products (TPs). 14 TPs were identified for 9 micropollutants, formed by cytochrome P450-mediated oxidation, conjugation and methylation reactions. The observed transformation pathways included reactions likely mediated by promiscuous enzymes, such as glutamate conjugation to mefenamic acid and pterin conjugation of sulfamethoxazole. For 15 compounds, including all azole fungicides tested, no TPs were identified. Environmentally relevant concentrations of chemical stressors had no influence on the transformation types and rates.