The Italian marginal areas of Orbetello and Lesina lagoons have been investigated in order to assess the response of benthic foraminifera to the trace element contents in the sediments. The investigated lagoons are deeply affected by high values of trace elements. The lagoon of Orbetello shows the highest values of Cd, Cu, Ni, Pb, Zn, and Hg, whereas the lagoon of Lesina exhibits the highest values of As. On the basis of the trace element contents, both lagoons can be considered from moderately to strongly polluted. Biotic and abiotic factors have been investigated with multivariate technique of statistical analysis. On the basis of the trace element content, the cluster analysis reveals the occurrence of three main clusters. These natural groupings are also confirmed by the principal component analysis. The comparison of trace element concentration patterns with the Foraminiferal Abnormality Index shows a possible influence of these pollutants on the benthic foraminiferal assemblages. Generally, the highest concentrations of trace elements in the investigated areas are remarkably mirrored by the highest percentages of deformed specimens.