Interstitial waters that have been recovered from the Sea of Japan down to a depth of 662 m below seafloor were analysed for B and δ 11B. B concentrations cover the range 0.12–3.37 mM (0.3–8 × seawater) and vary isotopically from +11.5 to +51.3‰ (relative to SRM 951 boric acid). Consistent concentration depth profiles demonstrate that the behaviour of this element is non-conservative and much more complicated during early diagenesis than previously thought. Small departures from seawater B concentration and isotopic composition in the core tops from sites in the Yamato Basin result from the desorption of an isotopically light B fraction. In the Japan Basin a large positive δ 11B anomaly seems to be related to the preferential adsorption of 10B in the depth range of more frequent ash layers. A large negative B anomaly seems to result from the alteration of volcaniclastic sands in a recently uplifted area. It seems that the thermal regime, in particular high heat flow, leads to B and Li maxima, δ 11B values lighter than seawater, and rather low Sr 87/Sr 86 ratios. B seems to be removed from pore waters at greater depth. It is finally incorporated into the sediment itself or altered basement rocks. Adsorption/desorption processes and alteration reactions within the sedimentary column and in the basement rocks govern the distribution of B in the pore fluids and should also influence the B content and isotopic composition of the alteration products, mainly clay minerals.