High‐altitude lakes are exposed to high fluence rates of solar ultraviolet radiation (UVR; 29–400 nm) and contain low concentrations of dissolved organic carbon (DOC). While in most lowland lakes, DOC can be used to predict UV transparency with sufficient accuracy, current models fail to estimate UVR in clear alpine lakes. In these lakes, phytoplankton may contribute significantly to the UV attenuation either as particles or as a source of chromophoric dissolved organic matter (CDOM) with distinctive properties. We investigated a series of 26 lakes in the Alps and Pyrenees, situated at elevations ranging from 422 to 2,799 m above sea level and having DOC concentrations ranging from 0.2 to 3.5 mg L⁻¹. CDOM, as measured by the absorptivity of filtered lake water, explained most of the variability in the attenuation of underwater UVR among lakes (r² = 0.94, P < 0.001). However, within‐lake variation in the UV attenuation revealed a significant contribution from phytoplankton in deeper waters (UV attenuation increasing with chlorophyll a concentration; r² = 0.97, P = 0.002), only apparent when DOC concentrations were low (∼0.3 mg L⁻¹). The DOC‐specific absorptivity (a_g^*) was also important for characterizing the optical conditions in this series of lakes. Epilimnetic values of a_g^* were significantly lower in lakes located at high elevations (with low allochthonous CDOM inputs from the catchment), compared to lakes surrounded by trees and meadows. Moreover, a_g^* was generally lower in surface waters than in deeper water layers, suggesting the influence of photobleaching on UV transparency. The slope S of the exponential regression between CDOM absorptivity and wavelength did not show clear patterns, such as found in marine systems, and often presented lower values in the epilimnetic waters (in association with lower a_g^*). Collectively, our results suggest that in transparent alpine lakes, the dynamics of the CDOM pool and phytoplankton production will have a strong effect on temporal changes in UV underwater attenuation.