Intensive prawn aquaculture in tropical regions is associated with high concentrations of total ammoniacal nitrogen (TAN) as a result of high rates of prawn excretion and feed loading. Excessive TAN can adversely effect productivity and result in adverse impacts on coastal waters. Cultures of indigenous nitrifying bacteria were enriched from intensive prawn aquaculture pond water using continuous and batch enrichment techniques. Cultures were capable of TAN removal over a wide range of initial TAN concentrations - up to 200 mg/l. Cultures were immobilized onto porous clay pellets to enhance cell density and applied to culture medium and TAN-augmented pond water under aerobic conditions to determine TAN removal proficiency. Immobilized cultures were able to achieve a high TAN removal proficiency in pond water - even at a low density of 0.1 pellet per liter. A concentration of less than 0.5 mg TAN/l could be maintained under a fed-batch condition of 3.2 mg TAN/1 per day, after an initial 2-day lag phase. A simplified and effective culture enrichment process was developed for culture immobilization onto pellets using TAN-augmented pond water. Overall, pellet immobilization of indigenous nitrifying bacteria represents a potentially effective TAN control system for prawn aquaculture in low-cost, but intensive tropical prawn farms.