Ecosystems are subsidized with inputs of mass and energy from their surroundings. These allochthonous inputs regulate many ecosystem characteristics. In inland waters, terrestrial inputs of organic matter regulate food-web structure, ecosystem metabolism, water clarity, and thermal stratification. Future changes in allochthony may be especially pronounced in high-elevation ecosystems due to increases in vegetation and precipitation associated with climate change. Several techniques exist to characterize the degree of allochthony of organic matter in aquatic systems, including metrics such as ΔH, the net isotopic discrimination between water and particulate organic matter (POM) of deuterium stable isotopes, and the fluorescence index (FI), which characterizes the fluorescence of dissolved organic matter (DOM). Despite the importance of allochthonous organic carbon inputs, little is known about either how allochthony varies across elevation gradients or whether different metrics are similarly related to allochthony. We measured AH, FI, and a suite of related water-quality characteristics in 30 lakes across a montane to alpine elevation gradient (2340 to 3205 m) in the Beartooth Mountains of Montana and Wyoming, USA, to understand how FI and AH varied with elevation, with one another, and with other allochthony-related water-quality characteristics. We hypothesized that allochthony of POM and DOM would decrease at higher elevations, with alpine lakes above treeline being more autochthonous compared with low-elevation lakes below treeline. We observed a significant inverse linear relationship between AH and Fl, with both metrics indicating a decrease in allochthony at higher elevations. Characteristics including the natural log of the ratio of concentrations of dissolved organic carbon to chlorophyll a (ln(DOC: Chl)), the spectral slope ratio between different spectra of two wavebands (SR, ratio of spectra at 275-295 to 350-400 nm), and a ratio of diffuse attenuation coefficients at 320 and 380 nm (KR, Kd320: Kd380) varied with both ΔH and FI while pH varied only with ΔH. High-elevation systems were characterized by low ln(DOC: Chl) and K(R), and high S(R) and pH. These results indicate that high-elevation lakes are more autochthonous than low-elevation lakes. The relationships among ΔH, FI, elevation, and other water-quality characteristics provide important insights to understand future changes in carbon cycling in mountain ecosystems.