Abstract In this study, we contrast the fluorescent properties of dissolved organic matter (DOM) in fens and bogs in a Northern Minnesota peatland using excitation emission matrix fluorescence spectroscopy with parallel factor analysis (EEM-PARAFAC). EEM-PARAFAC identified four humic-like components and one protein-like component and the dynamics of each were evaluated based on their distribution with depth as well as across sites differing in hydrology and major biological species. The PARAFAC-EEM experiments were supported by dissolved organic carbon measurements (DOC), optical spectroscopy (UV-Vis), and compositional characterization by ultrahigh resolution Fourier transform ion cyclotron resonance mass spectroscopy (FT-ICR MS). The FT-ICR MS data indicate that metabolism in peatlands reduces the molecular weights of individual components of DOM, and oxygen-rich less aromatic molecules are selectively biodegraded. Our data suggest that different hydrologic and biological conditions within the larger peat ecosystem drive molecular changes in DOM, resulting in distinctly different chemical compositions and unique fluorescent fingerprints. PARAFAC modeling of EEM data coupled with ultrahigh resolution FT-ICR MS has the potential to provide significant molecular-based information on DOM composition that will support efforts to better understand the composition, sources, and diagenetic status of DOM from different terrestrial and aquatic systems. Spectral characteristics of five components of Dissolved Organic Matter (DOM) in Glacial Lake Agassiz peatland porewaters identified by PARAFAC modeling of EEM fluorescence spectra. Color contours reflect intensities expressed in Quinine Sulfate Equivalent (QSE) units; blue low, red high. The relative loadings of these components to total fluorescence vary as a function of peat type and depth, and appear to be a function of the quality of the DOM and the active microbial community present.