The use of live feed is common in aquaculture processes due to its nutritional advantages, and rotifers comprise one of the most used feeds in finfish aquaculture. However, bacteria present in water used for rotifer culture are a significant source of infection and consequently diseases could cause mortality in fishes. Advanced oxidation process (AOPs) are methods that may be useful to eliminate bacterial infections present in aquaculture wastewater and may allow the reuse of this water. Therefore, the prospect of using different advanced oxidation processes to inactivate Vibrio spp. and total bacteria cultures (TCB) present in this kind of water was evaluated. In particular, UVc/O3/H2O2, UVc/H2O2 and O3/H2O2 and the adsorption process were applied to seawater coming from a fish farming tank. The results obtained were highly promising because it was possible to inactivate 100% of bacteria present in the seawater when UVc/ozone/hydrogen peroxide and UVc/hydrogen peroxide were applied, needing around 20 and 80 min for Vibrio spp. and total culturable bacteria inactivation, respectively. These results are justified due to the strong action between H2O2 in the presence of UVc, which may produce a large amount of hydroxyl radicals. Nevertheless, when ozone/hydrogen peroxide was applied, total inactivation of bacteria did not occur. Also, an interesting relationship between bacteria inactivation and oxide reduction potential of seawater was observed during the process. Rotifers put in water after the treatment did not suffer behavior changes (swimming) and no mortalities were observed.