Twenty-nine sediment samples were collected from the Hurghada Bay, a heavily polluted bay on the Red Sea of Egypt, to inspect the environmental quality status and anthropogenic consequences on benthic foraminifera. Some foraminiferal species showed deformations in their apertures and coiling directions as a response to environmental stresses. In addition, the FoRAM index, an index used for evaluating the growth of coral reefs, indicated a hazard in the proximity of nearshore stations. To elucidate the relationships between the biological response and chemistry of sediments, eight heavy metals concentrations (Cu, Cd, Zn, Pb, As, Cr, Ni, and Mn) were analyzed using inductively coupled plasma–atomic emission spectrometers (ICP-AES). Interestingly, two groups of benthic foraminiferal associations were illustrated using multivariate statistical analyses. Group I have extremely high heavy metal concentrations, an enriched total organic matter (TOM)%, high deformation percentages, and mud content. Moreover, it is dominated byAmmonia tepidawhich is regarded as an opportunistic species. Group II includes low to moderately polluted stations, highly enriched living foraminiferal assemblages, and is dominated by the sensitive rotaliidsNeorotalia calcarandAmphistegina lobifera. Alternatively, four geochemical indices, EF, CF,Igeo, and PLI, are used to assess the contamination level that shown ominous spots for the nearshore stations of the Hurghada Bay. The pollution indices (HQ and HI) were also conducted to evaluate the risks of carcinogenic heavy metals on human health. Our findings demonstrated that ingestion and dermal exposure have greater carcinogenic hazards for adults and children than inhalation. The lifetime carcinogenic risk (LCR) is significantly higher than the permissible limit and follows this order: Pb > As > Cr > Cd > Ni. To that end, developing strategies to lessen the negative impact of pollution on human health and/or the Red Sea’s biodiversity is an inevitable issue in the present day and future.Supplementary InformationThe online version contains supplementary material available at 10.1007/s11356-023-27242-4.