In order to assess the response of benthic foraminifera to trace element pollution, a study of benthic foraminiferal assemblages was carried out into sediment samples collected from the Santa Gilla lagoon (Sardinia, Italy). The lagoon has been contaminated by industrial waste, mainly trace elements, as well as by agricultural and domestic effluent. The analysis of surficial sediment shows enrichment in trace elements, including Cr, Cu, Hg, Ni, Pb and Zn. Biotic and abiotic data, analyzed with multivariate techniques of statistical analysis, reveal a distinct separation of both the highly polluted and less polluted sampling sites. The innermost part of the lagoon, comprising the industrial complex at Macchiareddu, is exposed to a high load of trace elements which are probably enhanced by their accumulation in the finer sediment fraction. This area reveals lower diversity and higher percentages of abnormalities when compared to the outermost part of the lagoon.