We attempted to estimate potential habitats of Clithon retropictus and to determine the community structure of benthic macroinvertebrates by presence of C. retropictus. 2016 to 2018 database of “Survey and Assessment of Estuary Ecosystem Health” by the Ministry of Environment were used to identify the distribution site of C. retropictus. The occupancy model was applied to estimate the potential habitat of C. retropictus. Four diversity indices were used to confirm the community structure of benthic macroinvertebrates. C. retropictus was found in the southern coast area and part of the east coast, and this pattern was consistent with previous studies. Additionally, the occupancy model predicted that a potential habitat of C. retropictus could appear in the west coast area. The community structure of benthic macroinvertebrates was relatively high at the site with C. retropictus than the site without C. retropictus. Therefore, the occupancy model can be considered when conserving C. retropictus inhabiting a limited area. Additionally, C. retropictus can be used to the indicator species that can represent the brackish water environment.