Biomonitoring of estuarine pollution is the subject of active research, and benthic foraminifera are an attractive group to use for these purposes due to their ubiquitous presence in saline water and wide diversity. Here, we describe a case study of biomonitoring using benthic foraminifera in the French Mediterranean lagoon, Bages-Sigean lagoon. In this case, the major pollutants of interest are heavy metals in the sediment, particularly contaminated by Cu and Cd derived from industrial and agricultural sources. The foraminiferal assemblages of the Bages-Sigean lagoon are typical of normal paralic environments, but unusually almost completely lack agglutinated forms. The density of benthic foraminifera was shown to be more influenced by the sediment characteristics rather than heavy metal pollution. However, the relative abundance of Quinqueloculina bicostata was shown to increase in the most polluted areas and we propose that this taxon may be used as an indicator of heavy metal pollution.