Flood magnitude in riverine systems has been increasing due to global climate changes in the world. The change of flow regime could greatly affect the riverine fish assemblages in a variety of the ways. It is difficult to conduct conventional fish survey after flood events due to sampling safety. This study examined the flood effects on seasonal (July-October 2021) fish assemblage compositions and immigration/extinction dynamics in the downstream of the Haji Dam in the Gonokawa River using quantitative environmental DNA metabarcoding. Our results show that the fish assemblage compositions have seasonally changed in the river segment. The fish extinction rates in the study sites were negatively related to the distance to the dam from pre flood (July) to post flood (August), suggesting that the fishes could have been displaced into the downstream. In contrast, the fish immigration rates were not significantly related to the distance to the dam possibly because the weirs in the river segment prevented the upstream movement of the fishes. These results suggest that the flood events could affect the fish assemblages in the river segment, and the connectivity among the sites is important to increase the rescue populations (i.e., fish immigration) from the downstream.