Seaweeds have been studied as a bioremediation component to reduce eutrophication in aquaculture systems, but the potential and applications of seaweed aquaculture have not been fully evaluated. The present study aimed to advance the bioremediation and application potential of seaweeds in aquaculture by evaluating interspecific variations in low-salinity tolerance, phosphorus (P) content, and production of ultraviolet (UV)-absorbing compounds. Two species of Phaeophyceae (Padina australis and Sargassum hemiphyllum) were most tolerant to low salinities, suggesting that these species would be suitable for introducing into estuarine, brackish water aquaculture systems. Considering the growth and P content, Caulerpa sertularioides was most efficient in P absorption from the ambient seawater under the common seawater salinity of 35. Two species of Rhodophyceae (Acanthophora muscoides and Hydropuntia edulis) possessed the most UV-absorbing compounds, which would contribute to the reduction in the penetration of UV radiation into aquaculture water. These results show versatile merits of seaweed introduction into aquaculture systems and suggest that suitable species should be selected considering the purpose and efficiency.