Although crabs are effective indicator species for evaluating the health of estuarine environments, the relationship between crab communities and environmental conditions in temperate river estuaries is poorly investigated. This study aimed to clarify the physicochemical factors that affect crab fauna in temperate areas, as well as classify and characterize habitat based on the similarity of crab fauna. Data of crab fauna and physicochemical environmental factors were collected at 199 sites in two temperate rivers. These survey sites were spatially arranged to cover the estuarine zone (i.e., tidal freshwater to polyhaline water) and the intertidal zone (i.e., the high tide to low tide line). The result of a direct gradient analysis showed that salinity and median particle size, in particular, affected crab fauna. Moreover, the survey sites were classified into seven groups based on the similarity of crab fauna, which were modeled with moderate accuracy using three variables: salinity, elevation, and percentage of silt. From these variables, we were able to identify seven different habitat types: salt marshes covered with fine or coarse sediment, upstream zones with gravelly sediment, intermediate zones between salt marshes and tidal flats, sand tidal flats with scattered hard structures, monotonous sand flats, and mud flats. Our findings suggest that maintaining the salinity gradient and diversity of sediment grain size is necessary to conserve crab species diversity in temperate river estuaries. Effective ecosystem conservation in these areas needs to take into account the physicochemical conditions in the seven identified habitat types.
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