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Paleoenvironment and paleoclimate changes during the Little Ice Age (LIA) were investigated using sediments from Lake Hamana. This lagoon in central Japan is under a complicated climate system influenced by the East Asian summer monsoon (EASM), East Asian winter monsoon (EAWM), and strong typhoon events. Diatom assemblages and chemical components of a 1.3 m sediment core suggest historical events of rapid salination and cyclical ecosystem shifts accompanied by monsoon condition changes. Most research has indicated that Lake Hamana changed from a freshwater lake to a brackish lagoon because of the Meio earthquake in 1498 CE. However, based on results from the diatom assemblage and chemical components, this salination occurred because of changes in the Hamana paleoriver flow, and this change happened before the earthquake, around the mid-15th century. Furthermore, it is clear that Lake Hamana was an oligohaline lagoon before salination. The lithology of the lake sediments and the diatom assemblage changed during the LIA; sand, water, and total diatom contents decreased. However, the relative abundance of marine diatom taxa increased during the LIA. These changes were introduced by a weakening EASM coupled with low precipitation under low solar activity during the LIA. Several flood events represented by freshwater diatom taxa and magnetic susceptibility peaks co-occurred with strong El Nino events during the LIA. It is inferred that this strong El Nino during the LIA induced frequent typhoons causing floods in central Japan.