In China’s freshwater environment, the eutrophication phenomenon has become more and more serious in recent years. The changes of water quality may induce the variation of metal’s corrosion behavior. In this paper, carbon steel as common material of hydraulic structure was the investigated object, and its early corrosion behavior affected by microbes (algae and microbe) in eutrophic lakes was studied using immersion test, electrochemical measurements and infra-red spectrometry techniques. The experimental waters were natural eutrophic water and microbescleaned water. The former was fetched from eutrophic East Lake in Wuhan City, Hubei Province of China, and the preparation of later was making natural eutrophic water sterilized and algae removed by UV radiation. In order to present the changes of carbon steel’s corrosion behavior in natural eutrophic freshwater with and without microbes, comparative experiments were conducted in lab. Both weight loss method and electrochemical techniques showed that, the corrosion rates of carbon steel decreased in early stage for the influence of microbe existence. The analysis of infrared spectra indicated that, corrosion product on the surface of coupons taken from natural eutrophic water, mainly were δ hydroxyl ferric oxide, magnetic iron ore, γ hydroxyl ferric oxide, α hydroxyl ferric oxide and β hydroxyl ferric oxide, with relative concentration ratio of 1:0.314:1.003:0.634: 0.654. While corrosion product on the surface of carbon steel taken from the microbes-cleaned water, mainly were α hydroxyl ferric oxide and γ hydroxyl ferric oxide, with relative concentration ratio of 1:1.215.