The sedimentary record of Nautajärvi, a lake in Finland, is 6.6 m long and covers uninterruptedly annual laminations (varves) sediments back to 9852 a BP. The isolation of Lake Nautajärvi from the Baltic Sea basin occurred at 9625 a BP, and since then the rate of sedimentation has remained relatively stable, averaging 0.6–0.7 mm yr-1. Varves consist of wo layers, a dark biogenic layer of particulate to fine-grained organic matter deposited in summer and a pale clastic layer of detrital origin linked to snowmelt and spring discharge intensity, which depend on the severity and snow storage during the winter. This dataset contains the varve (annual) thickness record and thickness of the seasonal layers published in Ojala and Alenius (2005). Data were collected in 1999-2003 and covers a time interval from present to 9852 a BP. Data are at seasonal to annual resolution. Detailed microfacies analysis, varve counting, and varve and laminae thickness measurements were performed on a scanning electron microscope back-scattered electron images (SEM BSEI), X-ray radiographs, and digital line-scan image analysis. Varves were analysed in between 200 marker horizons 5-6 times using different media, and deviations between counts were registered to represent the margin of error associated within the varve chronology.