Lake Suigetsu (Japan) is a key site for radiocarbon (14C) calibration and palaeo-environmental reconstruction in East Asia. Here we present a description of the sediment (micro)facies, which in combination with a new approach to varve interpolation allows construction of a revised varve based chronology that extends the previous 2012 varve based chronology by ∼10 ka, back to ∼50 ka BP. Challenges in varve counting and interpolation, which were previously discussed in detail only for the Last Glacial-Interglacial Transition, are described here back to ∼50 ka BP. Furthermore, the relative merits of varve counting by μXRF scanning and by thin-section microscopy are discussed. Facies analysis reveals four facies zones, their transitions driven by both local and climatic controls. The lamination quality of the sediment is highly variable and varve interpolation reveals that in the analysed time interval, on average, only 50% of the annual cycles are represented by seasonal layers. In the remaining years seasonal layers are indistinguishable, i.e. either did not form or were not preserved. For varve interpolation an advanced version of the Varve Interpolation Program was used, which enabled the construction of the longest, purely varve dated chronology published, despite long intervals of poor lamination quality. The calculated interpolation uncertainty is +8.9% and −4.6%, which is well within expectations considering the high degree of interpolation and the length of the record.