The origin and degradation/preservation state of organic matter (OM) in lacustrine systems can be studied using its molecular composition. Pyrolysis gas chromatography-mass spectrometry (Py-GC-MS) allows rapid assessment of OM-rich samples and has proven a useful tool for peat, lacustrine and marine deposits, but is rarely applied specifically to lake environments prone to the formation of varves (annually laminated sediments), which are used frequently for palaeoenvironmental reconstruction. We applied Py-GC-MS to a 3.5 yr record of sediment trap samples collected from Nylandssjon in northern Sweden to determine the usefulness of the method for improving knowledge of OM dynamics in varved lakes. It appeared that seasonal variation controlled the pyrolysis fingerprints: intact polysaccharides and lignin from vascular plants, chitin from arthropods and chlorophyll from algae were concentrated in spring and summer traps, whereas winter trap samples were enriched mainly in degraded components, as OM slowly trickled down under a thick layer of ice. A secondary diagenetic process involving sulfurisation of phytadienes was recognised via isoprenoid thiophenes, with no clear seasonal trend, probably because it occurred under anoxic conditions at the lake bottom. The N-containing compounds from proteins in algae and chitin in arthropods were abundant in all samples, indicating that the dominant flux of varve OM was autochthonous in origin. We conclude that Py-GC-MS has significant potential for identifying the variability in parent material (source organisms and degradation state) and could become a valuable tool for palaeoenvironmental reconstruction from varved lake sediments.