Food consumption is increasing as the world population increases. While the eating of fish is spreading worldwide, the depletion of fishery resources has become a problem owing to overfishing, and the importance of aquaculture is increasing in order to continue to supply fish as food. In marine aquaculture, fish are grown in aquaculture cages in the sea. Thus, if a harmful algal bloom (HAB) reaches the cages, it will cause serious damage. Countermeasures against HAB are one of the important problems for aquaculture fishermen. In Nagasaki Prefecture in Japan, countermeasures against HAB include patrolling and sampling water by ships. These samples are then submitted to HAB experts for analysis. Following this analysis, notification is provided to aquaculture fishermen. When HAB is detected early, aquaculture fishermen can minimize the damage of HAB by stopping feeding and moving the aquaculture cages. In this study, we developed a system of early detection and notification of HAB to aquaculture fishermen. This is carried out by patrolling and sampling water using drones, detection of HAB by microscope and PC operation, and automatic notification by email and web application. As a result of this developed system, the identification accuracy of harmful plankton is more than 90%, and the time taken to find HABs can be shortened from the 6 h of the conventional approach to 15 min using this newly developed system.