Heterogeneous individual growth and cannibalism are major impediments to farming giant freshwater prawn (GFP), Macrobrachium rosenbergii, and growing GFP individually in compartment farming units could eliminate both hindrances. This study conducted two pioneering trials to evaluate a newly designed indoor compartmental grow-out system for GFP. The first trial was designed to investigate the potential use of three commercial microbial supplements (two Bacillus spp. and one photosynthetic bacteria) for water treatment. The results of ammonium removal efficiency showed that the bacterial supplements with Bacillus spp. had the highest ammonia removal efficiency of 91.73% and 90.57%, respectively, compared to the commercial photosynthetic bacteria (86.69%). The second trial evaluated the effect of four water flow rates at 1, 2, 3, and 4 L/min on the growth performance of GFP juveniles. The mean weight gain of the prawns grown in the compartments subjected to the flow rates of 1 L/min and 2 L/min (11.57±0.2 g. and 11.46±0.5 g) was significantly higher than the prawns grown in compartments where the water flow rate was set at 3 L/min and 4 L/min (9.91±0.55 g and 9.65±0.45 g). These results suggest that administration of Bacillus strain in the rearing water and optimal flow velocity confer beneficial effects in vertical compartment culture of GFP.