Different hypotheses have been tested about the fractionation and bioavailability of rare earth elements (REE) in mangrove ecosystems. Rare earth elements and bioavailability in the mangrove ecosystem have been of significant concern and are recognized globally as emerging pollutants. Bioavailability and fractionation of rare earth elements were assessed in Jazan and AlWajah mangrove ecosystems. Comparisons between rare earth elements, multi-elemental ratios, geo-accumulation index (Igeo), and bio-concentration factor (BCF) for the two mangroves and the influence of sediment grain size types on concentrations of rare earth elements were carried out. A substantial difference in mean concentrations (mg/kg) of REE (La, Ce, Pr, Nd, Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm, Yb, and Lu) was established, except for mean concentrations of Eu, Gd, Tb, Tm, and Lu. In addition, concentrations of REEs were higher in the Jazan mangrove ecosystem. However, REE composition in the two mangroves was dominated by the lighter REE (LREE and MREE), and formed the major contribution to the total sum of REE at 10.2–78.4%, which was greater than the HREE contribution of 11.3–12.9%. The Post Archean Australian Shale (PAAS) normalized values revealed that lighter REE (LREE and MREE) were steadily enriched above heavy REE. More so, low and negative values of R(H/M) were recorded in the Al Wajah mangrove, indicating higher HREE depletion there. The values of BCF for REEs were less than 1 for all the REEs determined; the recorded BCF for Lu (0.33) and Tm (0.32) were the highest, while the lowest BCF recorded was for Nd (0.09). There is a need for periodic monitoring of REE concentrations in the mangroves to keep track of the sources of this metal contamination and develop conservation and control strategies for these important ecosystems.