A simple, rapid on-line analytical method for the determination of plutonium (Pu) isotopes in soil and sediment samples was developed. Microwave leaching was used to extract Pu from the major sample matrix. L-Ascorbic acid was found to be the most appropriate agent to convert all the Pu to Pu(IV) for chromatography. Flow injection chromatography using TEVA resin was optimized to separate, preconcentrate and elute Pu from other constituents of the sample including 238U. An APEX desolvation unit with a PEEK Mira Mist nebuliser was used to minimize clogging and hydride interferences. The advantage of using a high sensitivity quadrupole ICP-MS instrument for Pu detection was demonstrated. The detection limit was found to be 3 and 0.3 pg kg−1 for 239Pu and other Pu isotopes, respectively, which corresponds to a theoretical detection limit of ∼10 mBq kg−1 for 239+240Pu. To demonstrate the applicability of the method, Pu activities and atom ratios were measured for different sediments from the northern Asian region.