Combining protein skimming with ozone (O3) is a common method for removing microparticles in recirculating aquaculture systems (RAS). Nevertheless, there is a limited number of studies that have validated protein skimming's performance at a commercial scale. Additionally, variations in protein skimmer designs and operational variables may yield different performance outcomes. In the present study, the performance of two types of full-scale protein skimmer (S1 and S2) were compared and evaluated under two levels of hydraulic retention time (HRT) (1.8 and 2.2 min) and three levels of O3 doses (0, 7, and 14 g O3/kg feed) in a commercial seawater RAS facility. Samples from the inlet and outlet of the protein skimmers were collected at each combination of operational variables. They were analysed for several relevant water quality parameters to quantify the treatment efficiency. O3 dose significantly improved water quality and reduced the numbers of microparticles and bacterial activity in a single pass. Besides that, doses as high as 14 g O3/kg feed significantly increased total residual oxidant (TRO) concentration. Additionally, an increase in HRT exerted a moderate effect on removing microparticles and a strong effect on redox potential (ORP) and TRO. Finally, the type of protein skimmer only affected the ORP, causing no significant changes to other water quality metrics. The correlations between the investigated water quality parameters defined a clear pattern of the ongoing processes and particle characteristics. Overall, the results demonstrated that protein skimming combined with carefully selected O3 doses can improve general water quality and control critical factors such as bacterial activity and microparticles under commercial operations.