This study aims to analyze the community of benthic foraminifera in the sediments of Manzala lagoon and investigate the impacts of trace metals on foraminifera. This lagoon is subjected to high input of anthropogenic pollutants from industrial, domestic and agricultural sources, which enter into the lagoon through some drains and canals. Twenty-four surficial sediment samples were taken by a grab sampler during February 2015. Some trace metals (Cu, Mn, Zn and Pb) were analyzed. Based on the contamination indices, Manzala Lagoon could be classified into three main regions: the southern part which exhibited the highest levels of pollution, the middle part of a considerable degree and the northern part of a low degree of pollution. Eight foraminiferal species, belonging to 5 genera were identified. The abundance of Ammonia beccarii and A. tepida may be due to the entrance of high inputs of freshwater into the lagoon and the prevailing of pollution (especially near drains). Test deformities are common and increased in the sites that exposed to pollution. The recorded modes of deformation include twisted tests, additional chamber, reduced chambers, aberrant chamber shape and size, twinning and complex deformities. Twisted or complex modes were common at the sites subjected to high levels of trace metals. This work supported the role of benthic foraminifera as an important bioindicator for the evaluation of the environmental quality of an ecosystem.