Benthic foraminifera are widely used to detect the health of their habitat, where they are very sensitive to even slight variations in the ecosystem. Therefore, the main objectives of this study are to examine the benthic foraminiferal assemblages in the sediments of Burullus Lagoon, evaluate the pollution levels and deduce the impact of trace metals on foraminifera. The continuous discharge of trace metals from agricultural, industrial and domestic sources into the lagoon may lead to a severe environmental problem. The concentrations of Mn, Cu, Cd, Zn and Pb within the sediments were measured. Recently, the assessment of contamination is principally based on the contamination indices which provide fast and simple quantitative values on the degree of pollution in a given aquatic environment. Thus, some indices, including the contamination factor, the degree of contamination, pollution load index, geoaccumulation index, ecological risk factor and potential ecological risk index are applied in this investigation. Based on the contamination factors, the sediments are very highly contaminated with Cd, considerably to very highly contaminated with Cu and Zn, moderately contaminated with Mn, low to moderately contaminated with Pb. All sites display very high values for the degree of contamination. Moreover, the values of the pollution load index are higher than 1, indicating that the lagoon is polluted. Depending on the geoaccumulation index, the contaminants are arranged as follows Cd>Zn>Cu>Mn>Pb. It is clear that Cd is the main contributor to the ecological risk factor in Burullus Lagoon. Concerning the richness of the foraminiferal assemblages, it fluctuates between 1–5 species per sample. Because of its higher tolerance to extreme conditions (changes in salinity and pollution), Ammonia tepida is the most abundant species. The occurrence of rare living individuals (25) is restricted only to sites close to El-Boughaz Inlet where higher salinity and lower levels of pollution are recorded. The same trend of distribution is shown by Cribroelphidium excavatum and miliolids, where they occur at sites with higher salinities. The occurrence of test deformities in all the studied sites may be related to the response of benthic foraminifera to trace metal. The forms of deformation include spiroconvex, reduced chambers, twisted tests, twinning, additional chamber and complex forms. The deformation depends on the nature of pollutants. Twinning and reduced chambers are the most dominant forms in areas close to the agricultural drainage (southern drains), while complex forms are abundant in areas close to industrial drainage (El-Gharbia drain). Thus, salinity and pollution may be the most regulatory factors controlling the distribution of foraminifera. This investigation confirmed the role of benthic foraminifera as a good ecological indicator in Burullus Lagoon.