Recent studies have demonstrated the importance of hydrological connectivity (surface or subsurface connectivity to river’s main stem) in determining biological and physicochemical properties of floodplain ponds. Nevertheless, mechanisms behind those patterns are rarely tested. Our study examined how the ecological integrity of floodplain ponds are maintained by high levels of surface hydrological connectivity, focusing on abundance, survival rates, and growth rates of universally imperiled freshwater unionid mussels. Field study was conducted in a low-land segment of Kiso River. A total of 68 ponds were selected within the segment, and surveyed to estimate the abundance of resident mussels and to measure various habitat variables. Both probability of occurrence and CPUE of mussels significantly increased with increasing frequency of inundation (FI) during floods. Three types of ponds with three replicates were selected and mussel individuals collected elsewhere were reared within enclosures: Type1, high FI with resident mussels; Type2, intermediate FI with mussels; and Type 3, low FI without mussels. Survival rates were significantly lowered with growth rates being almost zero in Type 3, where anoxic condition was frequently formed near the bottom. These findings suggest that frequent inundation have direct and positive effects on mussel habitat by preventing formation of low-oxygen conditions.