The effect of stratospheric ozone depletion on increases in ambient levels of solar ultraviolet (UV) radiation in high-latitude regions' has raised concerns about the response of northern ecosystems to environmental change. The concentration of coloured dissolved organic material, which is derived from terrestrial vegetation and acts as a screen for ultraviolet radiation, is low in high-latitude lakes. The underwater light environment in these lakes is therefore likely to be sensitive to small variations in the supply of this material, in addition to the effects of ozone depletion. Here we use fossil diatom assemblages in combination with bio-optical models to estimate the magnitude of past variations in the underwater light regime of a lake at the boreal tree line. We find large shifts in underwater UV-B, UV-A and photosynthetically available radiation associated with changes in the input of coloured dissolved organic material into subarctic lakes during the Holocene. The inferred changes in biological exposure to UV radiation were at least two orders of magnitude greater than those associated with moderate (30%) ozone depletion. Our findings indicate that freshwater ecosystems at present located across vegetation gradients will experience significant shifts in underwater spectral irradiance through the effects of climate change on catchment vegetation and the export of coloured dissolved organic material.