An electroosmotic flow (EOF) controlled counterflow isotachophoretic stacking boundary (cf-ITPSB) system under field amplified conditions has been examined as a way to improve the sensitivity of anions separated by capillary zone electrophoresis. The system comprised a high concentration of a high-mobility leading ion (100 mM chloride) and a low concentration of low-mobility terminating ion (1-3 mM MES or CHES) added to the sample in an unmodified fused-silica capillary at pH 8.05, buffered with Tris. Computer simulation studies using the software GENTRANS showed an increase in sensitivity of at least 10-fold over the previous cf-ITPSB system for simple inorganic ions, nitrite and nitrate. The simulations also suggested that the cf-ITPSB became stationary within the capillary and that its stationary position was not adversely affected by the concentration of MES. This was in contrast to experimental results that showed a slow and continual movement of the cf-ITPSB. This was more pronounced at lower concentrations of terminator (i.e., <3 mM) and resulted in a loss of resolution due to the cf-ITPSB being closer to the detector upon separation. This discrepancy was attributed to the change in pH across the capillary due to electrolysis and low buffering capacity in the sample, a phenomenon that cannot be simulated by the GENTRANS software. Replacement of MES with CHES as a lower mobility ion with increased buffer capacity failed to reduce the movement of the cf-ITPSB but did provide a further 3-fold improvement in sensitivity. The potential of this approach for sensitivity enhancement was demonstrated for the co-EOF separation of a mixture of six inorganic and small organic ions, with detection limits at the single-figure nanogram per liter level. These detection limits are 100,000 times better than can be achieved by normal hydrodynamic injection (ions prepared in water) and 250 times better than has been achieved by other online preconcentration approaches. The application of the EOF-controlled cf-ITPSB with counter-EOF separation of two pharmaceutical pollutants, naproxen and diflunisal, was also demonstrated with an improvement in sensitivity of 1000 giving detection limits of 350 ng/L in sewage treatment wastewater without any offline pretreatment.