Northern permafrost regions have vast stores of organic carbon (OC) and rapidly rising temperatures make these frozen soil OC stores increasingly vulnerable to thaw and mobilization. While considerable attention has been given to carbon export from large arctic river systems and lowland areas, significant gaps remain in identifying OC sources and mechanisms of processing and export at local scales and in alpine regions. Northern wetlands and lakes have been highlighted as critical areas for OC storage and processing, and while ubiquitous in alpine regions, there remains a lack of information on their role in the integrated response of watersheds. In this study, we utilize high frequency and repeat spatial sampling over four years to characterize the sources and transformations of DOC/DOM in the 169 km2 Wolf Creek Research Basin, Yukon. Optical indices were used to assess changes in DOM quality from alpine headwater streams, through lake and wetland complexes, to the outlet in low elevation boreal forest. High frequency measurements of CDOM captured event and intra-season dynamics. High SUVA254 /HIX in headwater streams indicated primarily humic/allochthonous DOM while comparatively lower SUVA254/HIX at the watershed outlet indicated predominantly autochthonous DOM. This downstream shift in DOM quality reflects the influence of a mid-catchment lake where high BIX and low SUVA254/HIX indicated autotrophic production of new DOM. Considering the complexing of DOM quality within a single representative watershed, results from this study help constrain projections of future DOM response and provide much needed process insights in a rapidly changing environment.