Recirculating Aquaculture Systems (RAS) reduce water consumption by efficient filtration to maintain appropriate levels of accumulating compounds and sludge. Sludge is mechanically separated by drum filters and disposed of to the detriment of overall system water budgets. Dissolved nitrogen compounds are reduced via nitrification–denitrification filters, requiring commercial external carbon sources. The reuse of sludge after ozone pre-treatment may represent the next step in RAS optimization. The present study analyzes the content of sludge from RAS and tests ozonation as a pre-treatment for recycling as carbon source. The dissociative effect of ozone and the physicochemical changes due to ozonation lead to a significant increase in soluble carbon availability. Predominantly long-chain fatty acid (FA) (saturated and unsaturated) with 16 and 18 carbon atoms independently of the treatment were found in the profiles. Saturated FA concentrations in solution increased after 20, 40, and 60 min ozonation. The solid content of the sludge was practically unaffected by ozonation in terms of FA profile: only saturated FA slightly increases after 40 min treatment. The implications of these findings for denitrifying bacteria are discussed.