Sediments and organisms were sampled to determine organotin contents – butyltins (BTs) and phenyltins (PhTs) – at 12 locations in an estuarine ecosystem, the Lagoon of Venice, characterised by varying contamination impacts. The results showed that organotin contamination in sediments is at lower levels, ranging from 2.5±0.1 to 84±1 ng g−1 (d.w.) for ΣBTs and from 0.8±0.2 to 7±1 ng g−1 (d.w.), for ΣPHTs, than in organisms, where the highest concentrations were found in filter feeders like mussels – from 60±3 to 7632±148 ng g−1 (d.w.) for ΣBTs and from 0.80±0.01 to 4005±121 ng g−1 (d.w.) for ΣPHTs. The possible risk to human health was assessed on the basis of the consumption of edible species sampled in some areas of the lagoon.