The risk of high river flow and peak storm surge superimposing in the estuary of small-and medium-sized rivers can be more severe during typhoon landfalls than at other times. In this study, 30 cases of typhoon track ensemble experiments for five rivers in Mikawa Bay, Japan, were evaluated using an atmospheric-river-ocean model. The results showed that storm surges coincided with high river flows when typhoons crossed the western side of Mikawa Bay, with the highest potential observed when typhoons passed northwest of the Bay. The average time discrepancy for the five rivers between the storm surge occurrence and increased river flow in the minimum time difference case was 48 min at the river mouth. Distinct trends in the time difference between a storm surge and river flow were observed for each river mouth. The order of time differences corresponded to the drainage area scale: Toyo (188 min), Umeda (112 min), Otowa (114 min), Sana (96 min), and Yagyu (88 min). Time difference trends also varied based on the distance between the typhoon center and each river mouth. For Toyo River, storm surges and high river flows did not substantially overlap, regardless of distance. However, for medium-and small-sized rivers, the time difference increased proportionally with the distance from the typhoon. The Yagyu River showed the highest potential for compound occurrence of a storm surge and river flood because of the synchronization of storm surge peaks and high river flow peaks, with a time difference of 1–2 h for small-and medium-sized rivers within 100 km2 of the basin.