Lake Kamo is an enclosed, low-inflow estuary connected to the open sea that is famous for oyster farming in Japan. In the fall of 2009, this lake experienced its first bloom of the dinoflagellateHeterocapsa circularisquama, which selectively kills bivalve mollusks. This species has been detected exclusively in southwestern Japan. The completely unexpected outbreak ofH. circularisquamain the northern region is believed to have been caused by the contamination of purchased seedlings with this species. The water quality and nutrient data collected by our group from July through October over the past 10 years revealed that the environment of Lake Kamo has not changed significantly. However, in the open water around Sado Island, where Lake Kamo is located, the water temperature has increased by 1.80 °C in the last 100 years, which is equivalent to 2–3-fold the world average. This has resulted in a rise in the sea level, which is expected to further deteriorate the water exchange between Lake Kamo and the open sea and low dissolved oxygen in the bottom layer of the Lake and the associated dissolution of nutrients from the bottom sediment. Therefore, seawater exchange has become insufficient and the lake has become nutrient rich, making it prone to the establishment of microorganisms, such asH. circularisquama, once they have been introduced. We developed a method to mitigate the damage caused by the bloom by spraying sediments containing theH. circularisquamaRNA virus (HcRNAV), which infectsH. circularisquama. After ∼10 years of performing various verification tests, including field trials, this method was used at the Lake in 2019. During the 2019H. circularisquamagrowth season, a small amount of sediment containing HcRNAV was sprayed on the lake three times, which resulted in a decrease inH. circularisquamaand an increase in HcRNAV, indicating that this method is effective in diminishing the bloom.