1. Aquatic organisms are adversely influenced by ultraviolet radiation (UV) and utilise photoprotective strategies, including pigmentation. We examined UV-protective melanin pigmentation of aquatic meiofauna (Cladocera) in relation to the UV exposure across 25 tree line lakes in Finland to address the potential effects of increased UV and altered input of UV-screening terrestrial dissolved organic carbon (DOC) on aquatic organisms. 2. Bio-optical parameters, including concentration of DOC, the coloured dissolved organic matter (CDOM) fraction, a suite of carbon quality indices and chlorophyll a, were analysed from lake water, and their role in controlling underwater UV environment (measured as diffuse UV attenuation coefficient K d at 305 and 340 nm) was examined. Cladoceran (Alona affinis) carapaces were extracted from the surface sediments, and their melanisation was assessed with spectroscopic UV-visible light absorbance measurements. 3. DOC, CDOM and specific UV absorbance (SUVA) had strong positive relationships with the attenuation of UV in the lakes, suggesting that terrestrial organic carbon controls underwater UV exposure in the examined lakes. The absorbance measurements indicated the presence of melanin in the cladoceran carapaces, the degree of melanisation varying strongly among the lakes. Melanisation had significant relationships with SUVA and fluorescence index (FI). It was higher in lakes with low SUVA and high FI, indicating that cladocerans exhibit strong melanisation in lakes with low contribution of UV-attenuating allochthonous DOC (i.e. high UV exposure). 4. The results suggest that cladoceran meiofauna respond to UV by utilising photoprotective pigmentation and that the degree of pigmentation is affected by site-specific underwater UV exposure, which is ultimately controlled by UV-attenuating DOC of terrestrial origin. 5. Although cladoceran meiobenthos are able to adapt to varying underwater UV doses, climate change with its multiple consequences on hydrology, limnology and catchment vegetation in the tree line zone may cause major changes in underwater UV environment for the organisms to adapt.