Microphysogobio rapidus is designated as endangered species class I by Ministry of Environment, and its distribution and population have been gradually declining, and it is now limited to the Nam River and some tributary streams of the Nakdong River Watershed. For the restoration of this highly endangered species, it is important to identify the causes of the decline and establish appropriate restoration plans. However, due to lack of basic data and ecological research, most steps are stagnant. Therefore, in this study, we identified the differences in the physical, biological, and sociological habitats between current and past distributed sites through field surveys and literature reviews. As a result of the field survey, there were differences in conductivity between the current and past distributed sites, and fish communities were also showed differences. The literature data also showed that the physico-chemical values of the past distributed sites were generally unfavorable, which generated negative consequences on biological factors. In particular, the effects of urbanization were found to be a major factor affecting the habitat of M. rapidus. Habitat stabilization is crucial for the recovery of this endangered species. However, in the past distributed sites, disturbances such as stream development and weir construction have altered streams physico-chemically and result in changes of M. rapidus. Therefore, a comprehensive plan that considers both stream connectivity and water quality is needed to manage and restore the habitat of M. rapidus.