<p>Using the results of the 40-year numerical experiment, we have investigated the processes of overturn circulation (OC) and its variability in Lake Biwa. In the severe winter of 2017–2018, OC begins as cold waters formed in the eastern shallow area descend the bottom slope to the deepest part. Even after the water column is homogenized, cold waters intermittently descend the slope causing the lateral transport and mixing of the lake water. In the mild winter of 2018–2019, vertical mixing and slope current do not reach the deepest part and OC ends incompletely. The remaining bottom waters often form a bowl-shaped structure which is accompanied by a clockwise circulation driven by the northerly winds. OC will be incomplete when the yearly difference of the winter surface water temperature (SWT) exceeds the annual increase of the bottom water temperature (BWT). The former is related to the climatic variabilities such as El Niño, La Niña, and the Southern Oscillation and the Arctic Oscillation while the latter due mainly to the downward heat transport by wind mixing. The lake depth affects the behavior of OC by determining the intensity of the annual-cycle variability of BWT. The linear warming trend of water temperature may not have much effect on the behavior of OC in Lake Biwa today. Possible types of OC cycle are discussed, and compared with other lakes. Historical observation data have reasonably supported the model results.</p>