Tracking paleoenvironmental change and past event deposits is very important to evaluate the natural hazard spatially. This paper presents how the environment changes and implies the event deposit depending on the diatom assemblage change. To investigate paleoenvironmental change and identify the difference between tsunami and typhoon deposits, we analyze diatoms from the sediments in two coastal lakes in southern Japan where flood deposits have been linked to historical typhoon and tsunami events (Lakes Kawahara and Ryuo). The sediment cores extend from B.C.E. 500 to approximately C.E. 1000 and the downcore variation in diatom assemblages indicates a series of transitions from saline to fresher conditions in both Lake Kawahara and Lake Ryuo between approximately C.E. 500 and 1700. We observe an obvious deviation in diatom assemblages in event deposits previously identified to be either of tsunami or typhoon in origin. For the most prominent event deposit preserved in Lake Ryuo by the Hoei tsunami of C.E. 1707, the deposition of marine diatoms serves as evidence of marine flooding, while the subsequent deposition of soil and freshwater diatoms indicates the mobilization of terrigenous sediment during returning seaward flows. In contrast, the most prominent event deposit in Lake Kawahara is associated with freshwater flooding by the Kamikaze typhoon of C.E. 1281 and contains very low diatom abundances and a peak of freshwater taxa, followed by a peak in diatom counts potentially due to greater biological activity induced by a resultant influx of nutrients and re‐oxygenation during the event.