The flowthrough system, a daily water exchange, has high risk in fluctuation of water quality. Moreover, the risk could impact the seed productions, especially in grouper nurseries. Recirculation and bioremediation systems are satisfying technique to maintenance the water quality. The aim of this research was to analyse the effectiveness of flowthrough, recirculation and bioremediation systems in grouper nursery for water quality and grouper seed production. The research was conducted with three treatments and four replications as follows: A. flowthrough, B. recirculation and C. recirculation with bioremediation. The research was conducted in a completely randomized design for 40 days. The best water quality in treatment C: Salinity ranged from 30-35 g/L, ammonia reached 0.0726-1.8978 mg/L, and inhibited the growth of Vibrio spp. up to 2.580 CFU/mL. The results showed that the best average value was obtained by treatment C with a survival rate of 94.8±0.4%, length growth rate of 0.110±0.003 cm/day, weight growth rate of 0.175±0.013 g/day, specific length growth rate of 2.02±0.04%, specific weight growth rate 5.56±0.28%, total length 8.0 cm, total weight 7.91 g, and feed conversion ratio 0.73±0.07.