This study investigated the concentration fluctuation of organotin compounds in the Turbidity Maximum Zone (TMZ) of the Yangtze Estuary within a tidal cycle. Organotin concentrations varied greatly during the tidal cycle with dissolved organotins ranged from 39 to 682 ng Sn·L−1 and 40–1588 ng Sn·L−1, and particulate organotins ranged from 59 to 467 ng Sn·g−1 dw and 21–429 ng Sn·g−1 dw in TMZ water close to Hengsha Island and Jiuduansha Island, respectively. Meanwhile, the maximum levels of organotins appeared at each period of tidal transition, suggesting the tidal-driven pulsed exposure of organotins was prevalent in the estuaries. Besides, the organic carbon-normalized partition coefficients (Koc) of tri-organotins between suspended particulate matter (SPM) and aqueous phase were correlated with the phase distribution of natural organic matter (NOM). The dissolved tri-organotins were also associated with the properties of dissolved organic carbon (DOC) including aromaticity, hydrophobicity, and chromophoricity. Hence, pulsed exposure on organotins in the TMZ are highly dictated by the dynamic environmental conditions (i.e., SPM and NOM) with the tidal currents, which could further provide information to assess organotin ecological risks accurately in estuaries.