Understanding residual (i.e., total minus tidal) currents in coastal seas is important because the residual currents affect long‐term material transports. In the Seto Inland Sea, Japan (SIS), a Bungo Channel to Kii Channel sea level difference causes a horizontal pressure gradient in the SIS and thus affects the residual current in the SIS. This study applies a linear regression method to examine how the residual current responds to the Bungo‐Kii sea level difference. The residual current is obtained using the reciprocal acoustic transmission data collected in the eastern portion of the Aki‐Nada sea area in 2012. The residual currents are estimated in the following three periods: from 12 April to 9 June, from 15 June to 21 July, and from 20 September to 27 October. In the regression analysis, an additional term is included to account for the fortnightly variation of the tide‐induced residual current. More than 75% of the observed residual currents can be explained by the sea level difference and the fortnightly variation. For the three periods, the variations of the residual current along the acoustic transmission line are, respectively, 0.20 ± 0.01, 0.22 ± 0.01, and 0.30 ± 0.01 cm s−1 per 1 cm of the Bungo‐Kii sea level difference. The corresponding variations in the volume transport are 920 ± 149,
1,040±170, and
1,390±223 m3 s−1 per 1 cm sea level difference. Comparing with the wind‐induced volume transport, we find that the sea level difference can cause a comparable volume transport variation.