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The data presented in this article are related to the research article entitled “Atmospheric transport of nutrient matter during a harmful algal bloom”[1]. These data provide the concentration of nutrients (nitrate, ammonium and FeⅡ) in the atmosphere and their deposited flux in the East China Sea prior to the harmful algal bloom on May 3–8, 2006. They can be helpful for analyzing the source of nutrients causing the harmful algal blooms.