In this study, the aquaculture wastewater treatment was performed in 2 L working volume in batch scale with 14 days treatment period. Both ammonia and phosphorus were almost completely removed from the aquaculture wastewater for the first 7 days and the period of 14 days seems to be appropriate for batch scale experiment. In addition, treatment period lesser than 14 days would omit the re-inoculation of EM which would complicate the treatment performance in batch scale experiment. Data obtained from batch scale experiment yield experimental retention time and various inoculation concentrations of bioremediators which are useful for the development of aquaculture wastewater treatment in continuous scale which is important for the real world application. Ammonia and phosphorus concentration were shown to increase after 7 days of EM bioremediation treatment period due to the release of absorbed nutrient content from the microbial biomass as the EM entered stationary phase due to the depletion of substrate to sustain its growth.