The bioavailability and risk assessment of As were studied in sediments of the Yangtze River estuary (YRE). Results showed that residual fractions dominated the As partition (>85%), which attenuated overall bioavailability. After the residual fraction, As mainly partitioned into the Fe-Mn oxides fraction (3.16-4.22%). Arsenic bound to Fe-Mn oxides was higher in wet seasons. The carbonate fraction was minimal, which may result from the negative state presence of As in sediments. According to the risk assessment code, the YRE was classified as low risk. Additionally, the reduction of As(V) to As(III) may occur due to the reducing condition in wet seasons. Considering As(III) is more toxic and mobile, As bound to the exchangeable and Fe-Mn oxides fractions may have more potential ecological risk. Thus, the speciation and fraction should be both considered on the ecological risk of As in sediments of the YRE.