Rare earth elements (REEs) including Yttrium (Y) are commonly used as tracers of estuarine and oceanic mixing. The lanthanide series and yttrium are usually referred to as REYs. The geochemical behavior of REYs in estuarine environments is generally described as being non-conservative, with large-scale removal by particle scavenging. During mixing, partitioning of these elements occurs according to their source function and the stability of natural complexes, with heavy REEs typically forming more stable complexes than light REEs in solution. In this study, we compare the concentrations and partitioning of the 0.7 μm-filtered and 0.05 μm-filtered fractions of the dissolved REYs collected during the summers of 2017 and 2021 in the surface waters (< 3 m) of the St. Lawrence estuarine system (river, estuary and gulf) with those of the Saguenay Fjord, a tributary of the latter that drains the Mesoproterozoic rocks of the Canadian Shield. Whereas REYs do not mix conservatively in the St. Lawrence Estuary (SLE) in the summer, they nearly do so in the Saguenay Fjord (SF). REY concentrations are 2.5 to 6 times greater in the surface waters of the SF than those of the SLE at the same salinity and, in contrast to most estuaries including the SLE, the fjord waters are enriched in LREEs. The 0.05 μm-filtered REY concentrations are positively correlated with dissolved organic carbon (DOC) and chromophoric dissolved organic matter (CDOM) concentrations in the SF but independent of both DOC and CDOM concentrations in the SLE. The CDOM in the fjord differs from that of the estuary as it is more aromatic and has a higher molecular weight. The formation of strong REE-humate complexes stabilizes REY ions in the SF surface waters and impedes their adsorption to and scavenging by solid surfaces during estuarine mixing. The LREE enrichment in the SF surface waters most likely reflects the geology of the fjord's drainage basin, more specifically the exposed Mesoproterozoic granites and gneisses of the Canadian Shield that are enriched in LREE relative to the younger Paleozoic sedimentary rocks exposed along the St. Lawrence Lowlands.