<p>Heavy rainfall events can severely reduce salinity in enclosed seas and cause physiological stress to marine organisms such as bivalves, and their frequency and intensity have been in an increasing trend in recent years. In the study area, Nanao Bay, located on Noto Peninsula, Japan, several flood disasters associated with heavy rainfall occurred in recent years, and in some cases, extremely low salinity water was observed in the aquaculture ground. There is no river whose flow rate is monitored in the watershed, and the impact of heavy rainfall events on the environment of this bay remains to be fully understood. In this study, a coastal ocean model with a rainfall-runoff model was developed and optimized using the results of the field observations, and the influences of heavy rainfall events and winds on low salinity water dynamics and seawater exchange were numerically investigated. The results of the field observations showed the influence of two prevailing winds in this area on low salinity water dynamics; northeasterly winds caused low salinity water to stagnate at the bay head, while southwesterly winds quickly dissipated low salinity water. The results of the sensitivity experiments showed that estuary circulation was enhanced by southwesterly winds common in July–August while suppressed by northeasterly winds frequent in late summer. The coastal ocean model with the rainfall-runoff model well reproduced the low salinity water dynamics, suggesting that it would be useful for analyzing the impact of increased heavy rainfall on the coastal area.</p>