Isotopic and elemental analysis, Fourier transform infrared spectroscopy (FTIR), principal components analysis (PCA) and two dimensional (2D) correlation analysis, where core depth was used as perturbation, were used to study the diagenesis of organic matter (OM) in Lake Superior sediments. Changes in OM composition were examined at five lake stations over a depth range of 0–10cm. PCA results show that depth-related changes among sites are similar, leading to an increased contribution from inorganic (and possibly refractory aromatic organic) components at each site, and a loss of contribution from other organic components. Synchronous spectra reveal that aliphatic esters and carbohydrates are degraded significantly with increasing depth, leading to an increased contribution from clay/biogenic silica/inactive carbohydrates. Asynchronous spectra show that, in general, carboxyl groups, including aliphatic ester and amide in protein, are degraded first, followed by a group of carbohydrates and then aromatic compounds and/or the SiO framework in clay and biogenic silica. Site dependent compositional variation occurs and appears to be influenced by topography and geology, e.g. the delivery of a larger load of terrestrial inorganic silicate minerals to certain sites and re-suspension/re-deposition, leading to less intensive down core variation at mid-lake central and eastern basin sites. The study demonstrates the usefulness of FTIR coupled with PCA and 2D correlation approaches for exploring structural changes in sedimentary material during diagenesis.