The C. japonica is an ecologically important species in estuaries and brackish waters, as well as a very important fishery resource. However, the relationship between its habitation conditions and environmental factors remains unclear. We therefore made a habitat prediction model using GLM to define the environment of the C. japonica habitat of Lake Shinji, incorporating data acquired from 1982 through 1983 which measured population density, location, silt/clay content, ignition of physical environmental data, pH, dissolved O2 density, chloride ion concentration, and COD of the quality of the water. Our analysis showed that the standardization parameter ignition loss, measuring organic matter and carbonate content in the sediment, was the main effect in the predictive model (estimate -2.22) and had the greatest absolute value. Thus the C. japonica's distribution is dependent on ignition loss, in the predictive model. As for interaction terms modifying distribution, the dissolved O2 and silt/clay content ratio had the largest absolute value at -2.12. In addition, it was revealed that the environmental factors which limit population levels of the C. japonica every season are different. These results, while derived from C. japonica, also suggest that our GLM model is effective to more fully understand the habitation area of immobile benthoses in general.