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Alterations occurring in the effluent organic matter (EfOM) during ozonation could be detrimental depending on the final application of the treated effluent. In this work, the fate of EfOM in different ozonized wastewaters was assessed through the monitoring of general water quality parameters and organic fractions determined through size-exclusion chromatography combined with organic carbon detection (SEC-OCD) analysis. These different components of EfOM were distinguished based on relative molecular weights and assigned to fractions named as biopolymers, humic substances, building blocks and low molecular weight neutrals and acids. The significant abatement (60–90%) of an ozone-refractory micropollutant (MP) was employed as reference to simulate potential scenarios in which also the presence of these species is wanted to be attenuated. Ultraviolet absorbance at 254 nm (UVA254) and chemical oxygen demand (COD) reductions ranged from 40 to 80% and from 10 to 45%, respectively, for ozone doses between 0.6 and 1.0 mM, depending on the organic matter content (both dissolved and suspended) and alkalinity of the effluents. Dissolved organic carbon (DOC) analysis showed 21–27% reductions in Membrane bioreactor (MBR) effluents, whereas for conventional activated sludge (CAS) samples this value increased (6–35%) during the oxidative treatment. This was attributed to the continuous solubilization of humic substances, according to SEC-OCD results. Moreover, accumulation of lower molecular weight fractions such as building blocks or acids was observed in all the tested effluents, and attributed to the breakdown of largest EfOM fractions, mainly humic substances. Relationships proposed in this work between humic substances evolution, water quality (UVA254) and process parameters (immediate ozone demand (IOD), IOD-normalized hydroxyl radical exposure (∫[ OH]dt/IOD) and transferred ozone dose (TOD)) might be useful for EfOM variations estimations along ozonation.