Intensive fish farming discharges large amount of nutrients, the majority of which are composed of dissolved nitrogen in ammonium form, which promotes eutrophication in coastal waters. Macroalgae have been proven to effectively reduce the nutrients of fish farm effluents and at the same time increase the economic output of the aquaculture system when economically important species are utilized. In this study, the potential of three high value carrageenophytes (Kappaphycus alvarezii, Kappaphycus sp., K. striatum) to extract ammonium in fish farm effluent collected from a milkfish (Chanos chanos) fish cage was investigated. To establish economic viability of the integrated culture system, the effects of elevated total ammonia of fish farm effluent on the growth rate, phycocolloid content, and quality of these seaweeds were determined. Tank cultivation trials showed that the three carrageenophytes substantially reduced the ammonium content of the fish farm effluent (41-66% reduction efficiency) and consequently attained maximum daily growth rates of 4.41%, 2.90%, and 2.75% for K. striatum, Kappaphycus sp., and K. alvarezii, respectively. Their carrageenan content was improved. Carrageenan quality, however, was not significantly enhanced. Elevated ammonium in fish farm effluent did not adversely affect the performance of tank cultivated Kappaphycus; thus, future integration of these seaweeds in fish farms is feasible.