A new, highly sensitive and reliable two-dimensional matrix elimination ion chromatography (IC) method was developed for simultaneous detection of bromate, chlorite and five haloacetic acids. This method combined the conventional IC in first dimension with capillary IC in the second dimension coupled with suppressed conductivity detection. The first dimension utilizes a high capacity column to partially resolve matrix from target analytes. By optimizing the cut window, the target analytes were selectively cut and trapped in a trap column through the use of a six-port valve, while the separated matrix were diverted to waste. The trapped target analytes were delivered on to the capillary column for further separation and detection. Temperature programming was used to improve selectivity in second dimension column to obtain complete resolution of the target analytes. Compared to the performance of one-dimensional IC, the two-dimensional approach resulted in a significant increase in sensitivity for all target analytes with limit of detection ranging from 0.30 to 0.64μg/L and provided more reliable analysis due to second column confirmation. Good linearity was obtained for all the target analytes with correlation coefficients >0.998. The proposed method was successfully applied to the determination of oxyhalides and haloacetic acids in various matrices with recoveries ranging from 90 to 116% and RSD less than 6.1%. The method allows direct injection of samples and the use of columns with different selectivity, thus significantly reduces the level of false positive results. The method is fully automated and simple, making it practical for routine monitoring of water quality. The satisfactory results also demonstrated that the two-dimensional matrix elimination method coupled with capillary IC is a promising approach for detection of trace substances in complex matrices.