Boron (B) and chlorine (Cl) are widely distributed on the Earth’s surface and show distinctive geochemical behaviors. Cl behaves rather conservatively in oceanic environments while B is an excess-volatile and its distribution is sensitive to sediment absorption and organic matter degradation. The distribution of B, Cl and their isotopes in pore waters provide useful information for distinguishing between shallow circulation and deep origin fluid sources. Thirty-six sediment cores 0 - 5 m in length were sampled from a foreland accretionary prism offshore Southwestern Taiwan where strong bottom simulating reflectors (BSRs) and an abundance of mud diapirs were discovered. More than 350 pore water samples were separated and analyzed for B, Cl and other major ions. Four long cores were selected for B and Cl isotopic analysis. We found that the Cl in all cores varied less than 10%, suggesting no major hydrate dissolution or formation involvement at shallow depths in the study area. However, the B concentration changed greatly, ranging between 360 and 650 μM, indicating a possible sedimentary contribution during the early diagenesis stage. The B isotopic compositions were relatively depleted (~25 to 37‰) in these pore waters, implying the addition of sedimentary exchangeable B with low δ11B. The Cl isotopes showed rather large variations, more than 8‰, possibly related to the addition of deep situated fluids. In summary, the chemical and isotopic characteristics of pore waters separated from piston cores off Southwestern Taiwan suggest strong influence from organic matter degradation during diagenesis at shallow depths and the possible addition of deep fluids advecting through mud diapir channels at greater depths, causing a minor degree of hydrate dissolution / formation to occur at shallow depths. Further systematic investigation of pore waters δ18O and δD are needed in a future study.