The search for solutions to environmental pollution has been on the increase, with many questions recently as to which marine organisms can bioaccumulate trace elements in the marine ecosystem. Cadmium, Cr, Cu, Fe, Mn, Ni, Pb, and Zn concentrations in sediment, seawater, and seagrass compartments (root, rhizome, and leaf blade) were determined at Rabigh lagoon, Red Sea. This is to provide an insight into the potential of Cymodocea serrulata to bioaccumulate trace elements and as a good candidate to biomonitor these elements in a natural aquatic ecosystem. Results revealed significant variations in trace element concentrations across the three compartments of C. serrulata and the sites, with site S8 located in the most closed part of the lagoon recording the highest concentrations for all the trace elements. The translocation factor (TF rhizome/root = 1.00) of trace elements was higher in the root compartment. This implies that the root compartment is a better bioindicator of trace elements and has more potential to be utilized for biomonitoring. A significant positive correlation (p < 0.01) was established between the trace element concentrations in sediment, seawater, and the three compartments of C. serrulata except for Mn concentration in the compartments. The seagrass C. serrulata can be used for biomonitoring of trace elements in marine ecosystems as our results provide information on its capacity to bioaccumulate these elements. This is one of the key characteristics of a typical bioindicator of aquatic pollutants.