Changes in seawater carbonate chemistry including increased seawater carbon dioxide concentrations (pCO2), commonly known as ocean acidification (OA), can impact metabolic activities and phytochemical production in marine algae. While OA impacts typically reduce animal health, this study investigated the potential of OA-induced changes in methanol bioactivity from the macroalgae Ulva fasciata, to enhance larval European sea bass (Dicentrarchus labrax) aquaculture via increasing antimicrobial activity. After exposing U. fasciata to four pCO2 levels ~280, 550, 750 and 1050 μatm, macroalgae methanol extracts at pCO2–750 exhibited the highest total phenolic content (TPC), flavonoid content (TFC) and yielded the highest antioxidant and antimicrobial activities. After using extracts as a daily water additive for sea bass larvae, U. fasciata methanolic extract at pCO2–750 yielded the greatest reduction in pathogenic bacterial community and the highest survival rate for sea bass larvae. Sea bass larvae growth was also highest after exposure to methanolic extract of U. fasciata grown at pCO2–750, potentially due to higher TPC, TFC and polyunsaturated fatty acid levels. Such nutritional benefits may have been acquired by sea bass larvae via direct uptake or via indirect transfer, by which live feed (Brachionus or Artemia) consumed by larvae accumulated more nutrients. Our results suggest that pCO2–750 has a significant physiological impact on U. fasciata, potentially allowing macroalgae under OA conditions to function as nutritional supplements to increase the performance of sea bass aquaculture