The summer blooms of Karenia mikimotoi have recently tremendously damaged aquaculture industries in the Bungo Channel, western Japan. We statistically extracted meteorological variables correlated with the magnitude and timing of the summer bloom in Uwajima Bay and Saiki Bay located in the eastern and western coasts of the channel using data for ~13 y until 2017. We conducted field investigations in 2017 to understand the water quality characteristics in both bays. Meteorological conditions were almost totally similar, but K. mikimotoi population dynamics were different to varying degrees from year to year between both bays. Bloom timing significantly correlated with air temperature in March and April in Uwajima Bay and Saiki Bay, respectively. Bloom magnitude negatively correlated with hours of bright sunshine for 10 days before the bloom peak in Uwajima Bay and positively with precipitation and negatively with wind speed 5-10 days before the bloom peak in Saiki Bay. Field investigations showed that water temperature and salinity were always higher in Uwajima Bay and that nutrient concentration fluctuations were different in both bays. The present study indicates a possibility that meteorological factors influence K. mikimotoi population dynamics by means of water quality and local physical processes in both bays.