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The composition of organic matter (OM) exerts a strong control on biogeochemical processes in lakes, such as for carbon, nutrients and trace metals. While between-lake spatial variability of OM quality is increasingly investigated, we explored in this study how the molecular composition of sediment OM varies spatially within a single lake, and related this variability to physical parameters and elemental geochemistry. Surface sediment samples (0–10 cm) from 42 locations in Härsvatten – a small, boreal forest lake with a complex basin morphometry – were analyzed for OM molecular composition using pyrolysis-gas chromatography-mass spectrometry, and for the contents of twenty-three major/trace elements and biogenic silica. 160 organic compounds belonging to different biochemical classes (e.g., carbohydrates, lignins, lipids) were identified. Close relationships were found between the spatial patterns of sediment OM molecular composition and elemental geochemistry. Differences in the source types of OM (i.e. terrestrial, aquatic plant and algal OM) were linked to the individual basin morphometries and chemical status of the lake. The variability in OM molecular composition was further driven by the degradation status of these different source-pools, which appeared to be related to sedimentary physico-chemical parameters (e.g., redox conditions) and to the molecular structure of the organic compounds. Given the high spatial variation in OM molecular composition within Härsvatten and its close relationship with elemental geochemistry, the potential for large spatial variability across lakes should be considered when studying biogeochemical processes involved in the cycling of carbon, nutrients and trace elements or when assessing lake budgets.