AbstractTributyltin (TBT) and triphenyltin (TPT) concentrations in water samples from Tanabe Bay were found to range from 4–28 ng l−1 and 3–7 ng l−1, respectively. In fishing ports, the concentrations of TBT in surface water were similar to those in bottom water. However, in aquafarming areas with poor flushing, the concentrations of TBT in bottom water were higher than those in surface water. This suggested that the TBT in water samples is re-eluted from sediment. No difference in the concentration of TPT was observed between the surface and bottom waters. The concentrations of TBT and TPT in sediment samples ranged from 3–23 μg kg−1 dry weight and 2–37 μg kg−1 dry weight. TBT and TPT concentrations ranged from 3.1–100 μg kg−1 and 3.1–7.2 μg kg−1 in oysters and gastropods, and from 1.1–4.9 μg kg−1 and <0.2–3.9 μg kg−1 in fish, respectively. Organotin concentrations in biota were lower than the tolerable average residue levels (TARLs). Alternative biocides – i.e. diuron, chlorothalonil, dichlofluanid, irgarol 1051 and Sea-Nine 211 – were also detected in surface water, and chlorothalonil and irgarol 1051 were detected in sediment. The concentrations of these compounds in surface water and sediment were lower than those reported previously. Dichlofluanid, chlorotharonil and irgarol 1051 were also found at low levels in oysters and gastropods, and at ranges of 325–339 μg kg−1, 268–291 μg kg−1 and 43–49 μg kg−1, respectively, in fish; the concentrations in fish were close to the TARL levels.