It is known that the vertical structure of the river bed of the Chikugo River estuary makes complex structures of cohesive soil (gata-soil) and sand. In this study, we develop a new model of bed variation analysis in the river estuaries with complex structures of bed layers, and we clarify the mechanism of bed variation in the Chikugo River estuary during a flood. In the model, when the volume ratio of gata-soil is larger than the porosity of sand, bed variations are calculated by the GBVC flood flow analysis method and continuity equation of sediment which takes into account the discharge rate of sand and erosion speed of the cohesive material. On the other hand, when the volume ratio of gata-soil is less than the porosity of sand, variations of the river bed are calculated by continuity equation for sand. This is because sand and mixture of sand and gata-soil have different transportation mechanism and the gata-soil has great influence on the bed variation. The newly developed bed variation model provides good explanations for bed variation in the Chikugo River estuary.