Fifty surficial bottom sediments from the Al-Shuaiba Lagoon (80 km south of Jeddah City, eastern Red Sea, Saudi Arabia) were investigated for some major and trace metals to map their concentration distribution in the lagoon, shed light on their origin and controlling factors, and to establish potential risks to living organisms through comparison with sediment quality guidelines (SQGs). Statistical analyses allowed the division of metals into five associations: (1) Mg-Ca-Sr, (2) Al-Zn-Cr-Ni-Cu, (3) Fe-Mn-Li, (4) K and (4) Pb-Cd. Their distributions indicated that elevated values of Al, Mg, Fe, Sr, K, Mn, Li, Zn, Cr, Cu, Pb, Ni and Cd occurred in high intertidal areas and in mangrove sediments. These decreased gradually towards the deeper waters and inlet, except for Ca, which had its highest concentration in the centre of the lagoon. Major elements mainly appear to originate from the mineralization and evaporation of the lagoon's water, whereas trace elements appear to originate from wind-blown dust and runoff, with subsequent concentration in sediments aided by adsorption onto fine particles and organic carbon complexes. Enrichment indices and a pollution load index (PLI) indicated that the lagoon sediments were highly enriched with Sr, Pb and Cd, with the latter two and PLI being the highest at the eastern side of the lagoon. Comparison with the SQGs showed that the concentrations of Cu, Pb and Cd are higher than the effect range low (ERL) and threshold effect level (TEL), but are lower than the effect range median (ERM). This suggests that these metals might cause an occasional threat to the biota in the eastern part of the lagoon.