It is known that in the coastal area facing the Sea of Japan, winter storm is very severe due to strong wind from Siberia and the wave height attains to 6-7m during this period. Hence water level rise in a river entrance due to wave set-up may exceed 1m, which is considerably higher than average tidal amplitude in this region, 0.2-0.5m. However, due to much influence of complicated geographical processes on wave set-up height in a river mouth, quantitative investigations have hardly been done until now. In addition, the water level in a river mouth is complicatedly interacted among tidal motion, river discharge, ocean waves and so on, and hence it is difficult to make highly precise estimation. In this study, water level rise in the mouth of the Yoneshiro River in Akita Prefecture, Japan is investigated. Geographical features of the river mouth are greatly dependent on seasonal variation of major physical forces. Therefore, the characteristic of wave set-up is assumed to be different according to the season, and hence monthly variation of wave set-up is quantified. It is found in winter, the water level rise by wave set-up becomes approximately 10% of the deep water wave height, whereas this ratio decreases rapidly in summer due to flushing of sediment around the river mouth caused by frequent occurrence of floods.