Electrokinetic supercharging (EKS) has been used in the last few years as a powerful tool for separation and on-line preconcentration of different types of analytes. We have developed a valuable modification for EKS system, namely counter-flow EKS (CF-EKS) and applied it for the separation and on-line preconcentration of seven non-steroidal anti-inflammatory drugs (NSAIDs) in water samples. In CF-EKS, a hydrodynamic counter-flow is applied during electrokinetic injection of the analytes within the EKS system. This counter-flow minimises the introduction of the sample matrix into the capillary, allowing longer injections to be performed. Careful choice of the optimum counter-flow as well as the optimum injection voltage allowed the sensitivity to be enhanced by 11,800-fold, giving limits of detection (LODs) of 10.7-47.0 ng/L for the selected NSAIDs. The developed method was validated and then applied for the determination of the studied NSAIDs in drinking water as well as wastewater samples from Hobart city.