Boreal lakes are considered hot spots of dissolved organic matter (DOM) processing within the global carbon cycle. This study has used FT-ICR mass spectrometry and comprehensive data evaluation to assess the molecular differences of SPE-DOM between lake column water SPE-DOM and sedimentary pore water SPE-DOM in 10 Swedish boreal lakes of the Malingsbo area, which were selected for their large diversity of physicochemical and morphological characteristics. While lake column water is well mixed and fairly oxygenated, sedimentary pore water is subject to depletion of oxygen and to confinement of molecules. Robust trends were deduced from molecular compositions present in all compartments and in all 10 lakes ("common compositions") with recognition of relative abundance. Sedimentary pore water SPE-DOM featured higher proportions of heteroatoms N and S, higher average WC ratios in presence of higher DBE/C ratios, and higher average oxygenation than lake column water SPE-DOM. These trends were observed in all lakes except Ljustjarn, which is a ground water fed kettle lake with an unique lake biogeochemistry. Analogous trends were also observed in case of single or a few lakes and operated also for compounds present solely in either lake column water or sedimentary pore water. Unique compounds detected in either compartments and/or in a few lakes showed higher molecular diversity than the "common compositions". Processing of DOM molecules in sediments included selective preservation for polyphenolic compounds and microbial resynthesis of selected molecules of considerable diversity.