The Sea of Japan, surrounding Russia, the Korean Peninsula, and the Japanese Archipelago, is one of the most rapidly changing seas in the world. We measured carbon and nitrogen isotope ratios of zooplankton. We determined that the carbon stable isotope ratio has been decreasing over 15 years, and this trend was comparable to or slightly more rapid than the Suess effect, which is a signal of anthropogenic disturbance. Therefore, carbon dynamics are changing in the shallow coastal waters.