NOVELTY - A method for aqueous isolation of depolymerized lignin in high yield from a lignin-containing biomass composition (C1), involves: positioning the composition (C1) into a flowthrough thermal reactor chamber comprising an input opening and an output opening; contacting the composition (C1) in the thermal reactor with an aqueous fluid, under elevated temperature conditions to provide for lignin release and depolymerization; and collecting, from the output opening, the output aqueous fluid comprising the depolymerized lignin.    USE - For aqueous isolation of depolymerized lignin from lignin-containing biomass composition to form highly-purified soluble or insoluble depolymerized lignin composition, or a fuel comprising at least 20%, preferably 80%, especially 90% aliphatic and/or aromatic 7-18C hydrocarbons, or chemical compound or composition (all claimed).    ADVANTAGE - The method provides aqueous isolation of depolymerized lignin in high yield. The flowthrough elevated temperature conditions reduce or eliminate counterproductive recondensation/re-polymerization of the released depolymerized lignin, relative to non-flowthrough or batch conditions/methods. The process provides a highly-purified soluble or insoluble depolymerized lignin composition, or a fuel comprising at least 20%, preferably at least 80%, especially at least 90% aliphatic and/or aromatic 7-18C hydrocarbons, or chemical compound or composition. The process achieves isolation of depolymerized lignin of at least 70%, preferably 90%, more preferably at least 93%, especially at least 95% of the original lignin in the output aqueous fluid. The process decreases syringyl (S)/guaiacyl (G) ratio (greater than 60%) of the depolymerized lignin relative to the original lignin in the lignin-containing biomass composition. The process provides reduction in H, G and S lignin of pretreated solid residues progressed along with water-only flowthrough pretreatment time, as established by Fourier transform infrared (FTIR) and pyrolysis gas chromatography-mass spectroscopy (GC-MS) analyses; and successfully achieves enhanced lignin removal of approximately 86% (previously 70-75%) in aqueous phase. The process isolates lignin fractions with over greater than 90% purity under improved flowthrough conditions; achieves significant recovery (75~80%) of native lignin (insoluble fraction in aqueous phase) through flowthrough systems; and establishes flowthrough conditions for increased solubilization of lignin in aqueous phase. The process successfully achieves mass balance of lignin recovery; and provides the preferential removal and degradation of S-lignin over H and G-lignin as a result of water-only flowthrough pretreatment. The process successfully establishes molecular weight profiles of low molecular weight depolymerized lignin; successfully demonstrates HDO of inexpensive lignin to 7-9C cyclohexane derivatives (jet fuel range hydrocarbons); and achieves high yields of lignin conversion (38-45%) with excellent selectivity of HDO aromatic hydrocarbon products (90-98%).    DETAILED DESCRIPTION - A method for aqueous isolation of depolymerized lignin in high yield from a lignin-containing biomass composition, involves: positioning a lignin-containing biomass composition (C1) into a flowthrough thermal reactor chamber comprising an input opening and an output opening configured to provide for passage of an aqueous fluid through the reactor chamber, where the input opening is in communication with a source of aqueous fluid; contacting the composition (C1) in the thermal reactor with the aqueous fluid, under elevated temperature conditions to provide for lignin release and depolymerization, by flowing the aqueous fluid through the reactor chamber under the elevated temperature conditions, to provide an output aqueous fluid comprising released depolymerized lignin; and collecting, from the output opening, the output aqueous fluid comprising the depolymerized lignin. An INDEPENDENT CLAIM is included for an aqueous-based system for depolymerizing lignin in high yield from a lignin-containing biomass composition, comprising: an aqueous flowthrough thermal reactor chamber comprising an input opening and an output opening; and a source of heat to provide for an aqueous fluid at a raised temperature within the aqueous reactor.