A multidisciplinary approach has been adopted in order to investigate the bioaccumulation of metals and organometals in macrobenthic populations. A complete method coupling a sampling strategy and classification of benthic organisms with a performant analytical procedure for the analysis of both metals and organometals has been developed. A single sample preparation method using a TMAH extraction and species specific isotope dilution makes it possible to analyse metals and organometals in the same extract, which is especially interesting for situations where only a limited amount of sample is available. Low detection limits have been obtained in the range of 12–250 pg g⁻¹ for mercury and butyltin compounds and 0.4–50 ng g⁻¹ for metals with good precision (1–10% RSD) even for a very low mass of sample (0.02 g). This method has been applied for monitoring contamination and bioaccumulation of metals and organometals as well as the biodiversity and trophic structure of the macrobenthic population of the Adour Estuary (South-West, France). The benthic macrofauna diversity indicates that inner estuarine stations are moderately polluted whereas outer estuarine stations are less impacted. However, metals concentrations in both sediment and benthic biomass do not change drastically between stations. Moreover, the bioaccumulation has been determined in relation to the feeding guild of benthic organisms. The results demonstrate that higher bioaccumulation is generally observed for deposit feeders directly impacted by sediment contamination compared to suspensive feeders and predators. Biomagnification along the trophic levels was highlighted for MMHg but no significant trend was observed for the other metallic compounds.