Typical vertical profiles of ion-adsorption-type rare earth element (REE) deposits discovered in southwest Japan were studied by conducting speciation analyses, including X-ray absorption fine structure and laser-induced fluorescence spectroscopy combined with transmission electron microscopy and adsorption/desorption experiments. The results revealed that REE speciation, migration, and enrichment in weathered granite is largely controlled by soil pH, which in turn controls the variable charges of kaolinite, the REE host phase. Both the distribution coefficient Kd and the soil pH increase with depth. As a result, (i) REE dissolution and migration occur in the near-surface acidic environment of the upper layers, where hydroxyls of kaolinite basal surfaces and edges are deprotonated to a lesser degree, and (ii) REEs accumulate in the relatively high-pH environment below the surface, where hydroxyls of kaolinite basal surfaces and edges are deprotonated to a larger degree, producing REE adsorption sites with variable charges. An increase of soil pH to greater than 6 in deeper layers promotes inner-sphere complexation of REEs. Although inner-sphere complexation inhibits the ion-exchange extraction of REEs, the inner-sphere complexes can be still extracted by lowering the pH of the extraction solution. This fact, which indicates that the adsorption of both inner- and outer-sphere complexes is reversible, is important in terms of both (i) understanding vertical REE profiles in which the pH varies and (ii) the efficient recovery of REEs from REE-enriched layers at all depths in weathered granite.