Mass mortality of Seriola quinqueradiata was caused by a Chattonella bloom in summer 2010 in the southern area of the Yatsushiro Sea. We analyzed the diurnal records of the mortality occurrence and cell density of C. marina to examine the short-term mortality dynamics. In addition, a hydrodynamic model and Lagrangian particle tracking method were used to examine interregional differences in the mortalities. Mortalities were concentrated along the southern coast of Shishi Island and western coast of Nagashima Island in early July. In late July, mortalities occurred along the southern coast of Shishi Island and eastern coast of Nagashima Island. Severe mortalities occurred where the bloom (>100 cells ml−1 of Chattonella marina) appeared in both early and late July. Model results show that interregional difference of the bloom was controlled by the advection system in the Yatsushiro Sea. The consistent spatio-temporal pattern between fish mortalities and bloom dynamics indicates the potential benefits of real-time monitoring of harmful algae and assessing factors controlling hydrographic conditions to mitigate mortalities.