The presence and status of harmful algal blooms (HABs) in Japan are reviewed, revealing a decrease in red tides; however, toxic blooms are found to be increasing in western Japan. Environmentally friendly control strategies against HABs are also compared with integrated agricultural pest management. Very high densities (105–108 CFU/g) of algicidal and growth-inhibiting bacteria were found in biofilm on seagrass and seaweed surfaces and in surrounding coastal seawater. The situation in freshwater ecosystems is similar to coastal seas for toxic cyanobacterium, Microcystis aeruginosa, and aquatic plants. These findings offer new insights into the ecology of influential bacteria and harmful algae, suggesting that protection and restoration of native seagrasses and seaweeds in coastal marine environments should be implemented to suppress HABs. Diatom blooms were successfully induced with bottom sediment perturbation to prevent the occurrence of harmful flagellates such as Chattonella spp. and Alexandrium catenella in the Seto Inland Sea; however, this method requires robust and reproducible verification. “Sato-Umi” is a helpful concept for HAB control in the sea and freshwater ecosystems when adequately managed by people (e.g., appropriate bottom perturbation; protection and restoration of seaweeds, seagrasses, and aquatic plants; application of polycultures of fish, seaweeds, etc.).