The purpose of this study was to assess changes in the in-lake conditions of lake Kassjön, northern Sweden, in response to environmental and climate changes over the past ca. 6500 years. Sediment concentrations of different elements and biogenic silica (bSi) were measured with wavelength dispersive X-ray fluorescence spectrometry (XRF) and Fourier transform infrared spectroscopy (FTIR), respectively. The lake-water total organic carbon (LWTOC) content was inferred based on near-infrared spectroscopy (NIRS). The marine sediment was distinguished from the lacustrine sediment by higher dry bulk density, lithogenic element concentrations and Br content, and lower bSi concentrations. After lake formation, the dry bulk density, lithogenic element concentrations and metal contents decreased, while organic matter (OM), bSi and LWTOC increased. The main reasons for these changes are soil development and vegetation establishment. Spruce immigration around 3000 BP induced considerable changes to the sediment concentrations indicative of increased erosion versus weathering, and LWTOC declined. These changes are mainly related the different characteristics of spruce compared to birch. Human influences in the catchment were also clearly visible, but the rest of the sediment sequence demonstrated that natural changes can be of a similar magnitude. Overall, relatively small-scale, catchment specific processes seem to be more important for changes in the lake conditions than general climate change.