Decreasing Arctic sea ice cover and increasing stratification of ocean surface waters make the exposure of pelagic microalgae to high irradiances more likely. Apart from light being a necessary prerequisite for photosynthesis, rapidly changing and/or high irradiances are potentially detrimental. An in situ study was performed in the high Arctic (79°N) to determine the effect of high irradiances in general, and ultraviolet radiation (UVR, 280–400 nm) in particular, on cell concentrations, fatty acid composition, and photoprotective pigments of three diatom species isolated from seawater around Svalbard. Unialgal cultures were exposed in situ at 0.5- and 8 m-depth. After 40 h, cell concentrations of Synedropsis hyperborea and Thalassiosira sp., were lower at 0.5 than at 8 m, and the content of the photoprotective xanthophyll-cycle pigment diatoxanthin in all species (S. hyperborea, Thalassiosira sp., Porosira glacialis) was higher in the 0.5 m exposure compared to 8 m. In S. hyperborea, growth was additionally inhibited by UVR at 0.5-m depth. In situ radiation conditions led, furthermore, to a significant decrease in polyunsaturated fatty acids (PUFAs) in all three species, but UVR had no additional effect. Hence, we conclude that natural radiation conditions close to the surface could reduce growth and PUFA concentrations, but the effects are species specific. The diatoms’ potential to acclimate to these conditions over time has to be evaluated.