A fully automated flow-through microcolumn fractionation system with on-line post-extraction derivatization is proposed for monitoring of orthophosphate in solid samples of environmental relevance. The system integrates dynamic sequential extraction using 1.0 mol l-1 NH4Cl, 0.1 mol l-1 NaOH and 0.5 mol l-1 HCl as extractants according to the Hietjles-Lijklema (HL) scheme for fractionation of phosphorus associated with different geological phases, and on-line processing of the extracts via the Molybdenum Blue (MB) reaction by exploiting multisyringe flow injection as the interface between the solid containing microcolumn and the flow-through detector. The proposed flow assembly, capitalizing on the features of the multicommutation concept, implies several advantages as compared to fractionation analysis in the batch mode in terms of saving of extractants and MB reagents, shortening of the operational times from days to hours, highly temporal resolution of the leaching process, and the capability for immediate decision for stopping or proceeding with the ongoing extraction. Very importantly, accurate determination of the various orthophosphate pools is ensured by minimization of the hydrolysis of extracted organic phosphorus and condensed inorganic phosphates within the time frame of the assay. The potential of the novel system for accommodation of the harmonized protocol from the Standards, Measurement and Testing (SMT) Program of the Commission of the European Communities for inorganic phosphorus fractionation was also addressed. Under the optimized conditions, the lowest detectable concentration at the 3σ level was ≤ 0.02 mg P l-1 for both the HL and SMT schemes regardless of the extracting media. The repeatability of the MB assay was better than 2.5 % and the dynamic linear range extended up to 7.0 mg P l-1 in NH4Cl and NaOH media and 15 mg P l-1 whenever HCl is utilized as extractant for both the HL and SMT protocols.