The assessment of sediment contamination is of crucial importance for the management of estuarine ecosystems. Environmental risk assessment of oil pollution must be specific to these ecosystems because of their unique toxicant bioavailability dynamics, which is not comparable with that of other ecosystems where the environmental parameters are less variable. The goal of this work was to test in two European estuarine areas (Ria de Aveiro, Portugal; La Manga, Spain) whether the common methodology used to evaluate sediment pollution in marine sediment (amphipod toxicity tests and community structure analysis) is suited to these physico-chemically unique systems. Manipulative field experiments were conducted at three oil concentration levels, to compare resulting changes in community structure with laboratory and in situ amphipod toxicity tests carried out with native amphipod species Corophium multisetosum (Atlantic area) and Microdeutopus gryllotalpa (Mediterranean area). The impact of the toxicant was reflected in the community structure and toxicity tests, both of which were correlated with oil concentration. These results point to this methodology being a reliable tool for assessing and monitoring pollution in estuarine areas.