The primary objective of this study was to track reactor gas emissions and microbial population dynamics during the acclimation of a bench scale SBR system operating via the nitrate shunt, defined here as the oxidation of ammonia to nitrite with denitrification of nitrite to nitrogenous gases, to elucidate potential strategies for overcoming the acclimation response. Aerobic phase nitrite accumulation was induced by periodically subjecting the nitrite oxidizer population to an expected inhibitory concentration of free ammonia under anoxic conditions as previously described by Turk and Mavinic (1986, 1987, 1989a, 1989b.A lab scale sequencing batch reactor (SBR) was operated with a pre-anoxic fill and high pH to subject nitrifiers to free ammonia concentrations reported to be inhibitory during the start of the aerobic phase. The anoxic period pH (and therefore free ammonia concentration) was controlled by adjusting influent feed pH via a combination of sodium hydroxide and sodium bicarbonate addition. This was the same pH control scheme used by others (Turk and Mavinic (1986, 1987, 1989a, 1989b) who have successfully operated systems via the nitrate shunt. The target anoxic zone free ammonia concentration was 8-to-10 mg NH 3 -N/L. The aeration rate was initially kept constant and the aerobic phase dissolved oxygen level was used as a gauge of nitrifier health. Tracking studies were conducted during several SBR cycles both during the shunt period and following the collapse of the shunt (acclimation), in order to elucidate the differences in process response, over and above nitrite accumulation. Changes in reactor microbial populations were tracked using a combination of slot blot hybridization and fatty acid analyses.The control of anoxic free ammonia concentration through influent pH adjustment resulted in nitrite accumulation followed by eventual process acclimation and complete nitrite oxidation. Nitrite oxidation was initiated at free ammonia concentrations far in excess of the inhibitory range reported by Anthonisen et al. (1976). By the time the shunt had collapsed, nitrite oxidation was initiated at free ammonia concentrations exceeding 9 mg-N/L. The period of nitrite accumulation was coincidental with reactor nitrous oxide emissions.RNA and suspended solids data suggest that the entire nitrifier population was severely compromised when the initial feed pH adjustment was made to increase free ammonia concentration and initiate the nitrate shunt. The drop in RNA binding nitrifier molecular probes (Nso 190, Ntspa 454, Ntspa 685 and Nb 1000 probes) coincided with an increase in effluent suspended solids. A drop in RNA concentration of this magnitude suggests the death and lysis of cells. The drop in total RNA suggested the entire population was compromised; however, the nitrite oxidizer population as measured by the Ntspa 454, Ntspa 685 and Nb 1000 RNA probe concentrations was most affected. The establishment of a new suspended solids equilibrium in 820 the reactor supports the possibility that the change in pH ...