We are developing a highly sensitive and selective on-chip chromatography-based chemical sensing system, which has the capability to detect most common ions, such as nitrite, nitrate, fluoride, chloride, phosphate and sulphate, in drinking and underground water, with the sensitivity of PPM to PPB level, and within a few minutes or even fractions of a second. The proposed system consists of two major parts: on-chip chromatography system and chemical sensing system. The integrated chromatography system is built with parylene microfluidic technology. Two sensing techniques, one based on conductivity, the other on surface plasmon resonance (SPR), are being explored for their exceptional sensitivity and miniaturization capability.