Ultraviolet-visible absorption and fluorescence spectroscopies allow simultaneous detection of several organic substances. These spectra also contain information on whether the organic matter is produced in the water body or in its catchment. In this work various spectral indices, which are widely used in aquatic studies to determine humic substances, proteinaceous matter, chlorophyllous pigments and the origin (autochthonous versus allochthonous) of organic matter, were applied to track changes in a Holocene record from the large and shallow northern temperate Lake Peipsi (Estonia/Russia) at a highresolution scale. Absorption and three-dimensional fluorescence spectra of the organic matter fraction dissolved in sediment pore water (pDOM) were analysed. In addition to the spectral measurements of pDOM, the sediment samples were analysed for main constituents (water and organic and mineral matter) and magnetic properties. The core chronology was established by nine radiocarbon datings. Temporal changes in pDOM in the record were quite variable; however, three periods in the development of the lake can be distinguished: a 2500 yr period in the early Holocene and a 2500 yr period in the late Holocene, when drastic changes in the accumulated matter occurred, and a rather stable 5000 yr period in between. We postulate that the changes over the period in the early Holocene reflect a rise of water level in the lake; the oscillations over the relatively steady period were probably caused by climatic factors, and alterations over the period in the late Holocene were due to the expansion of agricultural activity in the lake catchment. Our findings indicate that the use of spectral indices in palaeoinvestigations offers valuable information for reconstructing natural and human-induced developments of lakes.