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Geochemical and mineralogical analyses of bottom sediments collected from Al-Shuaiba (SHL) and Al-Mejarma (MJL) coastal lagoons, Red Sea were carried out. Mineralogically, the sediments consist mainly of carbonate minerals particularly aragonite, high and low Mg-calcite and traces of dolomite admixed with non-carbonate minerals including quartz, k-feldspars, plagioclase and traces of amphiboles, mica and clay minerals. The spatial distribution of major and trace elements at the bottom of the lagoons indicates two groups of elements. The first, less significant, is of terrigenous origin concentrates mainly in the shoreward direction. This group includes the silicates (Al2O3-Fe2O3-SiO2), Feldspars (K2O-Rb-Ba) and heavy minerals (V-Cr-Zr, TiO2-Y-Nb) related elements. The second most dominant group is the carbonate related elements (CaO-Sr) that concentrates in the seaward direction. The two lagoons are not affected by urbanization or anthropogenic impact, and hence the siliciclastic elements are related to the terrigenous influx mainly by aeolian transportation. The carbonate related elements are mainly of biogenic origin related to calcareous skeletal remains. The elemental distribution in the bottom sediments of the MJL is more homogeneous than those in the SHL reflecting the bottom conditions that are mainly controlled by lagoon morphology, hydrodynamic and the water circulation between the lagoon and the sea. Geochemical data show no obvious enrichment of Al-normalized redox-sensitive trace elements V and Cr suggesting that there is no variation in the bottom redox conditions in contrast with other previous studies. The information in this work is an important tool for biogeochemical and biological research projects in the Red Sea coastal lagoons.