Change in flow regime due to global climate changes can significantly affect riverine fish assemblages. Understanding relationships between species abundance and occupancy at large spatial scale is important for estimating future fish species extinction due to global environmental changes. However, conventional survey (e.g., seining sampling) is time consuming and labor intensive and it is difficult to conduct the fish survey at basin scale. This study examined relationships between fish abundance and occupancy in the Takatsu River in Japan in preflood (June) and postflood (October) of 2022, using quantitative environmental DNA (eDNA) metabarcoding. We hypothesized that (1) fish species with higher abundance (i.e., higher eDNA concentration) could have higher occupancy (i.e., higher eDNA detection rate at the entire basin), (2) fish species with higher abundance could have higher persistence (i.e., exist both months), and (3) the abundance-occupancy patterns could vary with fish ecological function (i.e., benthic fishes vs. non-benthic fishes). Our results indicated that fish species with higher eDNA concentrations tended to have higher occupancy at the basin scale. In addition, fishes with higher eDNA concentrations had higher persistence in the study sites throughout the months. Further, non-benthic fishes with low abundances could be more affected by flood event than benthic fishes with low abundances.