The Yangtze River Estuary (YRE) is strongly influenced by the Yangtze River and lies on the pathway of the East Asian Monsoon. This study examined atmospheric deposition and air-sea gas exchange fluxes of dichlorodiphenyltrichloroethane (DDT) and hexachlorocyclohexane (HCH) to determine whether the YRE is a sink or source of selected pesticides at the air-water interface under the influences of river input and atmospheric transport. The air-sea gas exchange of DDT was characterized by net volatilization with a marked difference in its fluxes between summer (140 ng/m2 /d) and the other three seasons (12 ng/m2 /d), possibly due to the high surface seawater temperatures and larger riverine input in summer. However, there was no obvious seasonal variation in the atmospheric HCH deposition, and the air-sea gas exchange reached equilibrium because of low HCH levels in the air and seawater after the long-term banning of HCH and the degradation. The gas exchange flux of HCH was comparable to the dry and wet deposition fluxes at the air-water interface. This suggests that the influences from the Yangtze River input and East Asian continental outflow on the fate of HCH in the YRE were limited. The gas exchange flux of DDT was about fivefold higher than the total dry and wet deposition fluxes. DDT residues in agricultural soil transported by enhanced riverine runoff were responsible for sustaining such a high net volatilization in summer. Moreover, our results indicated that there were fresh sources of DDT from the local environment to sustain net volatilization throughout the year.