A recently developed hyphenated system for "organic" size-exclusion chromatography-pyrolysis-gas chromatography-mass spectrometry (SEC-Py-GC-MS) is adapted to allow the use of aqueous LC eluents as applied in the characterization of water-soluble polymers. The system uses syringe-based transfer of multiple LC-fractions to the GC instrument with solvent elimination and subsequent pyrolysis in a programmed temperature vaporization injector. The problems of the large-volume injections of aqueous, salt containing eluents into the Py-GC-MS are solved by using a 'sintered-bed liner' for elimination of the water at a high temperature, a volatile salt and the installation of a back-flush option. After optimization, the system was applied for the determination of the combined molecular weight-chemical composition of a polyethylene glycol-polypropylene glycol block copolymer. This analysis was done with the system in the aqueous SEC-Py-GC-MS mode. Also demonstrated is the automated at-line characterization of a random polystyrene-polymethylmethacrylate copolymer, now with the system in the gradient reversed-phase LC-Py-GC-MS mode. The methods proposed in the present work are very useful for the detailed characterization of water-soluble copolymers.