The littoral topography of the coastal lagoons in Japan have been developed mainly under the influences of the sea level change in the Holocene. And they have been also affected by the human activity especially in the last 2000 years. In this paper the author showed some case studies about the environmental changes in the three coastal lagoons ; Lake Saroma, Lake Abasiri and Lake Hamana. At first in Lake Saroma well-developed lacustrine terraces and wide littoral shelves were focused in relation to the sea level change in the Late Holocepe. And also in this lake the author referred to a small island which was present about 150 years ago but now has aready been eroded and submerged. Secondly in Lake Abashiri the geomorphological development of the Abashiri river delta in the last 300 years were clarified based on a topographical classification map and an old map drawn about 150 years ago. Lastly in Lake Hamana we have obtained an evidence which indicates that a big earthquake occurred in 1498, by means of the echo-sounding survey in the northern part of the lake.