The nitrogen in the aquaculture wastewater can have significant effects on receiving water bodies like eutrophication and ammonia toxicity to fish communities. Removing nitrogen by nitrification-denitrification can reduce the potential impact of aquaculture wastewater discharge. Nitrification is affected by different factors including dissolved oxygen, temperature, pH, alkalinity, toxicity, unionized ammonia and substrate concentration. All these parameters affect ammonia-oxidizing and nitrite-oxidizing bacterial activity. The aim of this work is to study the effect of the carbon source on nitrifying bacterial activity in an activated sludge treating aquaculture wastewater. An activated sludge (AS) system was set up and operated continuously for 180 days. The operation was divided into two phases. During Phase I a source of organic carbon (CH 3 COONa) with a C/N level of 2.4 (operation days 1 to 101) was fed into the system, while in Phase II a source of inorganic carbon (NaHCO 3 ) with a C/N level of 16.2 was fed into the system (operation days: 102 to 180). The maximum NH 4 + -N removal efficiency was 49.7% during the Phase I, during which the NO 3 - -N and NH 3 + -N concentrations were 37.1 ± 14.0 and 2.9 ± 1.1 mg/L, respectively. In Phase II, the maximum NH 4 + -N removal efficiency was 45% and NO 3 - -N and NH 3 + -N effluent concentrations were 2.8 ± 0.3 mg/L and 210 ± 49 mg/L, respectively. Ammonia- and nitrite-oxidation decreased in Phase I from 0.231 ± 0.005 mg NH 4 + /gVSS min to 0.018 ± 0.004 mg NH 4 + -N/gVSS min and in Phase II from 0.049 ± 0.011 mgNO 2 - -N/gVSS min to 0.010 ± 0.002 mgNO 2 - -N/gVSS min.