Rare earth elements (REE) have unique chemical properties, which allow their use as geochemical tracers. In this context, the present study aims to assess the role of Funil Reservoir on REE biogeochemical behavior. We collected water samples upstream of the reservoir (P-01) in the city of Queluz, inside the reservoir (P-02) and downstream of Funil Reservoir (P-03) in the city of Itatiaia, RJ. In the field, physicochemical parameters were measured using a probe (pH, temperature, electrical conductivity, and dissolved oxygen). In the laboratory, water samples were filtered (0,45 µm) and properly packed until chemical analysis. Chlorophyll a concentrations were determined by a spectrophotometric method and suspended particulate matter (SPM) by a gravimetric method. Ionic concentrations were determined by ion chromatography technique and REE concentrations were determined by ICP-MS. Chlorophyll a concentrations were higher in Funil Reservoir. Ionic concentrations in Queluz (P-01) suggest anthropic contamination. The sum of REE in the dissolved fraction ranged from 2.12 to 12.22 µg L− 1. A positive anomaly of La in Queluz indicates anthropic contamination. The observed patterns indicate that Funil Reservoir acts as a biogeochemical barrier, modifying the fluvial transport of REE. Nonetheless, another factor that probably influences REE behavior is the algal bloom that occurs in reservoirs during the rainy season. The seasonal behavior of algae can influence REE biogeochemistry through the incorporation and release of trace metals.