Two hazardous typhoons, Lionrock (August 2016) and Jebi (September 2018), destructively affected the coast of Japan and produced extreme sea level variations. The results of field surveys in the impacted regions showed that multiple deaths and extensive floods were caused by the combined effect of low-frequency sea level raise (storm surges) and intensive high-frequency (HF) tsunami-like waves (meteotsunamis). The data from ten tide gauges for the 2016 event and eight gauges for the 2018 event were used to examine the properties of the observed sea levels, to estimate the relative contribution of the two sea level components and to evaluate their statistical characteristics (maximum wave heights, amplitudes and periods of individual components, etc.). For the 2016 event, we found that the surge heights were from 12 to 35 cm and that the mean contribution of surges into the total observed sea level heights was ~ 39%; the meteotsunami amplitudes were from 22 to 92 cm, and they contributed 61% of the total height. For the 2018 event, storm surges were significantly stronger, from 46 to 170 cm, while HF amplitudes were from 38 to 130 cm; their relative inputs were 67% and 33%, respectively. Combined, they formed total flood heights of up to 120 cm (2016 event) and 288 cm (2018 event). Previously, the contribution of storm seiches (meteotsunamis) in coastal floods had been underestimated, but results of the present study demonstrate that they can play the principal role. What is even more important, they produce devastating currents: according to our estimates, current speeds were up to 3 knots (1.5 m/s) during the Lionrock event and more than 5 knots (2.6 m/s) during Jebi; these strong currents appear to be the main reason for the resulting damage of coastal infrastructure. The most important characteristic of the recorded meteotsunamis is their trough-to-crest maximum height. During the 2016 event, these heights at three stations were > 1 m: 171 cm at Erimo, 109 cm at Hachijojima and 102 cm at Ayukawa. The 2018 event was stronger; maximum meteotsunami wave heights were 257 cm at Gobo, 138 cm at Kushimoto, 137 cm at Kumano and 128 cm at Murotomisaki. The 2018 Gobo height of 257 cm is much larger than historical non-seismic seiche maxima for the Pacific coast of Japan (140–169 cm) estimated by Nakano and Unoki (1962) for the period of 1930–1956.