Display omitted •Microcontaminants eliminated (>99%) by ozonation but acute toxicity increased.•Acute toxicity was related to microcontaminant byproducts or other water components.•D. magna adaptation and reduction of chronic toxicity in S. capricornutum was observed.•Ozonation and membrane technologies could be combined to treat microcontaminants. The purpose of this work was to study the ozonation of nanofiltration (NF) retentates of real municipal wastewater treatment plant (MWTP) effluents for removal of microcontaminants (MCs) and toxicity. MCs present in these effluents were monitored using LC–MS/MS. Acute and chronic toxicity was addressed with Daphnia magna, Vibrio fischeri and Selenastrum capricornutum. Up to 40 MCs were found, most of them in concentrations over 100ng/L. 90% degradation of the sum of MCs was the critical point of comparison. When the NF membrane system was applied to MWTP effluents, treatment of NF rejection needed 2.75–4.5g O3/m3,4.5g O3/m3, which is less than 50% of the ozone needed for direct treatment of MWTP effluent. Treatment time (lower than 11min) was not influenced by MCs concentration, at least in the range tested (25–190μg/L). It has been demonstrated that consumption of ozone increased with organic load and inorganic content of different real effluents. MCs were eliminated by ozonation but acute toxicity (against V. fischeri and D. magna) increased. Chronic toxicity results were different and contrary in D. magna and S. capricornutum, due to the generation of new transformation products more toxic to D. magna than the parent contaminants. S. capricornutum inhibition percentage decreased in all cases after ozonation treatment. According to these results, before ozonation is implemented in MWTPs for the removal of MCs, the transformation products must first be examined and the treatment time or ozone doses should be extended to complete degradation if necessary.