Abstract. A bottom cold water mass (BCWM) is a widespread physical oceanographic phenomenon in coastal seas, and its temperature variability has an important effect on the marine ecological environment. In this study, the interannual variation of the BCWM in Iyo-Nada (INCWM), a semi-enclosed bay in the Seto Inland Sea, Japan, from 1994 to 2015 and its influencing factors were investigated using monthly observational data and a hydrodynamic model. The interannual variation in water temperature inside the INCWM showed a negative correlation with the area of the INCWM, and positive correlations with the local water temperature from April to July and with remote water temperature below 10 m in an adjacent strait in July. Differing from previously studied BCWMs, which had interannual variations depending closely on the water temperature before the warming season, the interannual variation of INCWM depends strongly on the air-sea heat flux during the warming season via local vertical heat transport and lateral heat advection. Further, by comparing several BCWMs, we found that the BCWM size is a key factor in understanding the mechanisms responsible for the interannual variation of BCWMs in coastal seas. These findings will help to predict bottom water temperatures and improve the current understanding of ecosystem changes in shelf seas under global climate change.