We investigated how the source and chemical character of aquatic dissolved organic carbon (DOC) change over the course of the runoff season (May–November, 1999) in Green Lakes Valley, a high‐elevation ecosystem in the Front Range of the Colorado Rocky Mountains. Samples were collected on North Boulder Creek from four sites across an alpine/subalpine ecotone in order to understand how the transition from the lightly vegetated alpine to the forested reaches of the catchment influences aquatic DOC. Concentrations of DOC at the four sites peaked between 2.6 and 8.9 mg C L−1 on the ascending limb of the snowmelt hydrograph, with the higher concentrations at the two subalpine sites. Seasonally, the chemical fractionation of DOC showed that there was a large range (29–72%) in the fulvic acid content of DOC at the four sites, with the highest fulvic acid percentages on the ascending limb of the hydrograph. Yields of DOC at the two gauged sites ranged from 10 to 11 kg ha−1 over the season with between 45 and 50% of the yield occurring as fulvic acid DOC and the remainder as nonhumic material. The fluorescence properties of DOC from all four sites indicated that during peak runoff, DOC was derived primarily from terrestrial precursor material. However, seasonal changes in the fluorescence properties of fulvic acids at the highest elevation sites suggest that DOC derived from algal and microbial biomass in the lakes is a more important source of DOC above tree line during late summer and fall. We hypothesize that much of the autochthonous DOC production is a result of algal growth in alpine lakes. Further, comparison to a forested control catchment suggests that processes in the alpine reach of the catchment may alter both the amount and chemistry of DOC incident to the downstream subalpine aquatic system.