Organotin (OT) compounds were determined in surface sediments and mussels Mytilus edulis from two major estuaries of the UK, the Mersey and the Thames, approximately one decade after legislation banning the use of tributyltin (TBT) compounds on small boats. Tributyltin concentrations in Mersey sediments ranged from 0·007–0·173 μg (as Sn) g−1 dry wt, increasing from the most upstream site, Fiddlers Ferry, towards the middle section of the estuary, and were highest at Stanlow, perhaps indicative of sources from the Manchester Ship Canal (MSC). A further peak in TBT concentrations occurred at New Brighton, opposite Liverpool Docks. Tributyltin was the predominant butyltin (BT) species in sediments (approximately 50%). Despite the fact that BTs represented only 4% of the total (HNO3-extractable) tin in sediments there was a linear relationship between these two tin compartments. Furthermore, BTs in mussels were correlative with total extractable tin in sediment, though in contrast to sediments, 85% of the total tin in mussels was made up of BTs, the most predominant of which was TBT. Concentrations of TBT in mussels increased from 0·058 μg Sn g−1 dry wt at the mouth of the estuary to 0·214 μg Sn g−1 dry wt at their upstream limit, close to the entrance to the MSC (Eastham). Triphenyltin (TPT) compounds were detected in only one sediment sample (New Brighton, 0·359 μg Sn g−1 dry wt) and one mussel population (Egremont, 0·022 μg Sn g−1 dry wt). Tributyltin concentrations in sediments from the Thames Estuary were marginally lower (0·002–0·078 μg Sn g−1 dry wt) than those found in the Mersey: highest concentrations were present in the upper estuary and decreased seaward. Again BTs contributed only a small percentage (<1% mean) towards the total tin loading in Thames sediments, but represented most of the tin burden (80%) in mussels. In contrast to sediments, TBT levels in mussels from the Thames Estuary were slightly higher than the Mersey (concentrations ranged from 0·100 μg Sn g−1 dry wt at the mouth to 0·302 μg Sn g−1 dry wt upstream) suggesting that TBT bioavailability is disproportionately higher in the Thames. Phenyltins were not detected in Thames samples.