The provenance of lake particulate matter in environmentally sensitive areas is crucial to understanding regional environmental and climatic changes. This study investigated two regions in the Northeast Tibetan Plateau, China: Region I (Keluke, Tuosu, and Gahai Lakes) and Region II (Qinghai Lake and nearby rivers). The results showed that: (1) The two regions have greater differences in the enrichment of rare earth elements (REEs) and heterogeneity in spatial distribution, both of which are characterized by relative enrichment of LREE and depletion of HREE, but to different degrees; (2) the source and formation of particulate matter in two regions are consistent. Particulate matter in Region I (Keluke and Tuosu Lakes) predominantly originates from granite rocks, which undergo weathering and transportation through rivers. Region II (Qinghai Lake and nearby rivers) particulate matter is affected by chemical weathering and partial recycling of detrital material. Diagenesis had a minimal impact on the particulate REEs. (3) This study primarily provides a preliminary understanding of REEs in lake particles, assessing particle changes during the water-to-sediment process and their provenance indication. Future studies will incorporate the solid fugacity (solid speciation) of REEs in particles, contributing to a comprehensive understanding of rare earth element geochemical processes. This study provides valuable insights into REEs distribution, source, and geochemical behavior in the Tibetan Plateau, underscoring the importance of REEs in understanding provenance processes, and is indicative of provenance studies in other climate change-sensitive regions of the world.