Pore waters were recovered from the sediment cores drilled in the back‐arc Amami Sankaku Basin (ASB) during the International Ocean Discovery Program Expedition 351. The sediment sequence is composed of the recent mud and ooze from late Oligocene/early Miocene accumulated at 7 m/Ma and rapid deposition of thick volcaniclastic sequence at 50 m/Ma. Such variations are reflected in the evolutions of chemical and isotopic compositions of pore waters. Cl and Ca concentrations in pore waters increased rapidly with depth and became enriched in the deep portion. Before arc rifting, extremely high deposition rates of volcaniclastic gravity‐flow sediments from the nearby Kyushu‐Palau arc into the ASB resulted in strong alteration, removing Mg and Si from pore waters. Mg concentrations were initially almost zero but abruptly shifted to substantial increases after ~29.5 Ma, indicating extended rifting of the active volcanic axis from the ASB. The δ18O and δD values of pore waters also evolved from more depleted and wide range to more positive and narrow range as a response to reduced alteration and increasing influence of seawater. Concentrations of Si and Mn in pore waters rapidly increased since ~29.5 Ma but suddenly declined at ~17.5 Ma due to the cessation of input of volcaniclastic materials. Covariations of Ca and Mg in pore waters are very similar to those in the back‐arc West Philippine Basin but significantly different from those in the Izu‐Bonin fore‐arc basin. Variations in chemical and isotopic compositions of pore waters can assist the reconstruction of tectonic activities.