Typhoons are a common feature of summer and autumn months in the East China Sea. These events often promote phytoplankton growth in surface waters as a result of upwelling and transport of nutrients, but their effects on sub-surface waters and ecosystems are little known. Furthermore, biological studies tend to focus on phytoplankton (using chlorophyll a assays), rather than on heterotrophic zooplankton. Indeed, measurements of biological and physicochemical changes induced by the storms are difficult to perform and risky, using standard shipboard sampling techniques. Using a camera mounted on an underwater, cabled observatory system in shallow coastal waters of Okinawa, Japan, we collected the first continuous, in-situ observations of the near-bottom, mesoplankton community during a series of typhoons. An increase in diatoms and radiolarians was found during all typhoons, whereas the response of larger zooplankton groups was variable between typhoons. A bloom of Trichodesmium cyanobacteria and diatoms was seen after a series of typhoons, while the total chlorophyll a concentration remained nearly unchanged at the sampling location. These findings shed new light on short-term responses of sub-surface ecosystems during typhoons.