Coastal ecosystems are significantly influenced by human activities within their river basins. However, the complex interplay of multiple factors makes it difficult to demonstrate causal links between individual drivers and ecosystem changes. This study focuses on two adjacent rivers, the Zuibaiji and Raizan Rivers, flowing through the Itoshima region near Fukuoka City, and their estuaries: the Imazu and Kafuri Tidal Flats. Despite similarities in geology, topography, and climate between these two river basins, and the presence of endangered species such as Horseshoe crab (Tachypleus tridentatus) and Black-faced spoonbill (Platalea minor) in both estuaries, notable differences exist. While the Imazu Tidal Flat has seen the extinction of the Asian hard clam (Meretrix lusoria), clam fishing continues in the Kafuri Tidal Flat. Analysis of factors contributing to these environmental differences revealed that, unexpectedly, there were no clear disparities in the degree of urbanization or in the water quality of the rivers and the adjacent coastal areas. However, clear differences were found in the impacts of dams, development around the tidal flats, and the environmental conditions of the bays facing the tidal flats. These findings suggest that overreliance on easily quantifiable indicators may lead to misinterpretations of environmental conditions. They also highlight the importance of clearly defining strategies, such as mitigating dam impacts and improving environments around tidal flats, for the restoration of coastal ecosystems.