The world is experiencing an increase in the frequency and intensity of extreme weather events, yet the influences of remote inland extreme weather events on the coastal ecosystem thousands of kilometers away remain poorly understood. Here we tracked the chain ecological effects of an extreme rainfall event in North China from terrestrial rivers to coastal aquaculture area of the eastern Shandong Peninsula. Our data suggest the autumn flood resulted from extreme rainfall event leads to abnormally low turbidity in the North Shandong Coastal Currents and coastal red tide blooms by introducing anomalous freshwater with an exceptionally high nitrogen-to-phosphorus ratio into the Bohai Sea. Lower salinity, stronger light conditions caused by limpid coastal currents, and phosphorus limitation resulting from red tide blooms account for huge kelp loss offshore of the eastern Shandong Peninsula. This study underscores the importance of considering multidisciplinary observation for risk management of unexpected extreme weather events.