We conducted numerical simulation of baroclinic currents due to two large floods in 2006 and 2012 from rivers located in the Ariake Sea, Japan in order to evaluate effects of climate change by global warming on regions of freshwater influence (ROFIs), in other word, baroclinic structure in the bay. As a result, the followings were clarified. Structure of residual currents in surface layer can be significantly affected by flood pattern from rivers. Especially, southward currents off Shimabara Peninsula are strengthened. Also, freshwater transport pattern can change due to flood pattern.