Background The simultaneous removal of carbon, nitrogen and phosphorus under variable operating conditions during the start-up period of a new multi-environment hybrid wastewater treatment technology called BioCAST is reported in this paper. The presence of both suspended-growth and immobilized microorganisms, as well as the continuous circulation of mixed liquor between the three zones of aerobic, microaerophilic and anoxic, supported high removal efficiencies of organic and inorganic contaminants. Results The removal efficiencies of carbon, nitrogen and phosphorus reached 99.3%, 98.0% and 92.3%, respectively, under varying organic loading rates in the range 0.43.0kgm-3 d-1, and nitrogen and phosphorus loading rates of 0.030.14kgm-3 d-1 and 0.0080.028kgm-3 d-1, respectively. Phosphorus removal increased steadily with the increase of nitrogen loading rate, producing a final effluent concentration of 2.9mgL-1. Low sludge generation was obtained along with a low biomass yield of 11.5%. Conclusions The start-up period of the BioCAST system demonstrated its potential for simultaneous removal of organic material, as well as nitrogen and phosphorus. Phosphorus removal demonstrated a strong dependence on nitrogen loading rate. Moreover, theoretical analysis of the liquid flow and energy balances in different zones of the treatment system showed that the pressure difference across the air diffuser is the governing force for the flow of liquid towards the aerobic zone and the controlling factor for the continuous circulation of mixed liquor among various zones. (c) 2012 Society of Chemical Industry