This study investigates the geochemical behavior and transport mechanisms of Rare Earth Elements (REEs), Yttrium (Y), Zirconium (Zr), and Hafnium (Hf) in three natural water systems under reducing conditions: the Santa Barbara and Occhio dell’Abisso mud volcanoes and a sulphureous spring at Villafranca Sicula. A comprehensive fractionation approach was applied to isolate the truly dissolved fraction (TDF < 10 kDa), the colloidal fraction (10 kDa < CF < 450 nm), the suspended particulate matter (SPM > 450 nm), and the associated bottom sediments. Analytical results reveal that REE distribution is significantly influenced by redox conditions and solid–liquid interface processes. The absence of negative Cerium (Ce) anomalies and the presence of pronounced positive Europium (Eu) anomalies in the Santa Barbara and Occhio dell’Abisso waters suggest strongly reducing environments where Eu²⁺ stability is enhanced. Shale-normalized patterns indicate that, while SPM and sediment fractions often exhibit Middle REE (MREE) enrichment, linked to Mn-bearing and Fe-oxyhydroxide phases, the dissolved phase reflects dissolution processes governed by a non-CHARAC (CHarge-and-RAdius-Controlled) behavior. Furthermore, the study highlights a significant decoupling in the Zr/Hf and Y/Ho pairs. While these pairs remain coherent during magmatic processes, they undergo mutual fractionation in aqueous systems due to differential reactivity toward colloidal surfaces and organic ligands. Specifically, Zr/Hf ratios in the colloidal and dissolved fractions deviate from chondritic values, driven by the preferential scavenging of Hf onto mineral surfaces. These findings underscore the utility of REE and Zr-Hf systematics as high-resolution tracers for reconstructing water–rock interaction processes and elemental cycling in complex hydrological environments.