Abstract The Shuaiba Lagoon is a fossil back-reef, hypersaline small basin located 80 km south of Jeddah city on the eastern Red Sea coast, Saudi Arabia. The surface sediments of the lagoon were investigated for their benthic foraminiferal content in order to correlate, in general, with environmental factors such as temperature, salinity, pH, sediment grain size, organic matter and, in particular, with tidal elevations to develop a training set for predicting sea-level changes in the lagoon. Hierarchical cluster analysis divided the benthic foraminifera in the Shuaiba Lagoon into four distinct faunal assemblages. Quinqueloculina cf. Q. limbata (Assemblage 1) and Monalysidium acicularis (Assemblage 2) assemblages dominated the intertidal–high subtidal areas (0.3 to − 0.5 m, LAT). The Peneroplis planatus–Sorites orbiculus Assemblage 3 occurred abundantly at all subtidal elevations (0 to − 1 m, LAT), whereas the Quinqueloculina costata – Spiroloculina communis – Elphidium striatopunctatum Assemblage 4 dominated the lowest elevations (