The high organic waste content of river water in Demak, north coast of Java, has caused traditional small-scale pond farmers to stop stocking shrimp. This paper examines whether seaweed and mussel will improve the quality of water these farmers use. The effect of Gracilaria verucosa and Perna viridis on the water quality was assessed by measuring the removal rates (RRs) of total organic material (TOM), total ammonia nitrogen (TAN), nitrite, and nitrate. The specific growth rates (SGRs) of seaweed and mussel were also measured. Thirty-six semi-outdoor tanks containing 800 L of brackish water and 7 cm substrate were randomly assigned to four replications of four densities of G. verucosa: 50 (S50), 100 (S100), 150 (S150), and 200 (S200) g m-2, and of P. viridis: 60 (M60), 90 (M90), 120 (M120), and 150 (M150) g m-2. Weekly, the TOM, TAN, nitrite, and nitrate contents were measured, seaweed and mussel weighted; RRs and SGRs were calculated at the end of the study. The effect of densities on the RRs was significant for both seaweed and mussel. P. viridis was more effective in reducing TOM (by 38%) than G. verucosa (7%); G. verucosa achieved higher RRs for TAN, nitrite, and nitrate. At S200, TOM and TAN decreased by 7.4% and 67%, respectively. At M90, TOM and TAN, decreased by 38% and 49%, respectively. However, nitrite increased significantly at S200 and M150. The SGR of seaweed was significantly lower at S200 than that at S150, S100, and S50. The best performing densities were S100 and M90.