Tributyltin (TBT) and its degradation products, dibutyltin (DBT) and monobutyltin (MBT), together with triphenyltin (TPT), were investigated in eels from the Thames Estuary and the Weston Canal (Merseyside). Within individual eels, the concentrations of organotin (OT) compounds varied considerably between tissues. Tributyltin concentrations were highest in heart and gall bladder and lowest in muscle and gonad. Tributyltin was generally the most predominant of butyltin (BT) compounds present in eel tissues and DBT the least. Phenyltins were detected in eels from both locations, notably the Weston Canal where TPT was present up to 0.367 μg g−1 (as Sn) in liver samples. Concentrations of OTs in liver (and muscle) were independent of weight and length in the eel populations examined. In a survey of OTs in eel populations along the Thames Estuary hepatic TBT levels ranged from 0.066–0.347 μg g−1 dry wt (as Sn) in liver of eels and were generally highest in the mid-section of the estuary, resembling the distribution pattern of TBT in sediment. Proportions of TBT to total BTs were also elevated in eel from this section of the waterway, consistent with continuing inputs in this region, albeit at relatively low levels. Major sewage treatment plants are sited here and may represent a possible source.