Mangrove forests are coastal wetland that can be sinks for material derived from terrestrial and marine settings. This study aims to establish the abundance, distribution, and enrichment of rare earth elements (REE) to track the sediment sources and infer biogeochemical processes occurring in the mangrove wetlands. Five sediment cores were collected throughout the Pichavaram mangroves in November 2010. The sampling sites were chosen based on vegetation cover, land-use pattern, and human interference. The vertical profile of the retrieved sediment cores were sub-sectioned, air dried, and homogenized into a powder before analysis. Higher REE concentration in Pichavaram sediments indicates dominance of input from the natural sources like weathering. Preferential REE enrichment was attributed to the alkaline pH (7–8.5) and reducing conditions prevailing in the mangrove environment allowing removal of MREE and LREE by adsorption and precipitation as Fe-Mn oxyhydroxides in sediments. Post Archean Australian Shale (PAAS)-normalized plots depicted convex subparallel shale-like patterns with similar enrichment. Pichavaram sediments showed strongly positive Eu anomalies, similar to that observed in Kaveri River sediments, validating the origin of REE in Pichavaram sediments as an outcome of natural weathering of post-Archean charnockitic and gneissic terrane. Also positive Eu anomalies indicated the prevalence of reducing conditions in Pichavaram. Cores near the estuarine mouth showed highly mixed vertical profile as compared to the undisturbed mangrove sites. Principal-component analysis delineated three main processes controlling REE distribution in Pichavaram, namely natural weathering, inherent physicochemical processes, and in situ biogeochemical processes occurring in this mangrove environment.