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Increased demand for rare earth elements (REE) has resulted in their increased exploitation and the need to better understand their cycling in aquatic environments. Thus far much of the research in boreal areas focused on REE cycling in larger rivers, while relatively little is known regarding their mobilization in smaller headwater streams. Here we used the Krycklan Catchment Study in northern boreal Sweden to investigate how REE are mobilized from diverse boreal headwaters and how their catchment exports are influenced by processes such as weathering, hydrology, and complexation with other solutes. We found that wetland dominated headwaters were source limited and prone to dilution during high discharge, while forested headwaters had considerably higher total REE concentrations and were less affected by discharge fluctuations. Larger downstream catchments showed clear discharge driven seasonal patterns, with high concentrations during spring flood and low concentrations during base flow. While the proportion of mineral soils and water travel time in the catchment were important predictors of REE mobilization, complexation with organic matter appears to play a greater role in higher-order streams with higher pH and a larger contribution from deeper groundwater sources. Overall, we highlight the stark differences between REE cycling in the headwaters and in higher order streams, which can provide important information on the processes that mobilize REE from catchments.