In the present study, the feasibility of a bioengineered two-stages sequential batch reactor (BTSSBR) followed by filtration-adsorption process was investigated to treat the agrochemical effluent by overcoming factor affecting process stability such as microbial imbalance and substrate sensitivity. An air stripper stripped 90% of toxic ammonia, and combined with other streams for bio-oxidation and filtration-adsorption. The BTSSBR system achieved bio-oxidation at 6 days hydraulic retention time by fending off microbial imbalance and substrate sensitivity. The maximum reduction in COD and BOD by heterotrophic bacteria in the first reactor was 87% and 90%, respectively. Removal of toxic ammoniacal-nitrogen by autotrophic bacteria in a post-second stage bio-oxidation was 97%. The optimum filtration and adsorption of pollutants were achieved at a filtration rate of 10 and 9 m(3) m(-2) h(-1), respectively. The treatment scheme comprising air stripper, BTSSBR and filtration-adsorption process showed a great promise for treating the agrochemical effluent. (C) 2013 Elsevier Ltd. All rights reserved.