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Aquatic ecosystems produce about 50% of the global biomass and play an important role in atmospheric carbon dioxide cycling. Since the primary producers are confined to the euphotic zone for energetic reasons, they are simultaneously exposed to short wavelength radiation. Solar UV affects growth, reproduction, photosynthetic production and many other physiological processes. Cyanobacteria are important ubiquitous prokaryotes which populate terrestrial and aquatic habitats. They account for up to 40 % of the marine biomass production and are important components of wet land ecosystems such as rice paddy fields. These organisms are also highly impaired by solar UV, but they and other motile microorganisms have developed mitigating strategies to protect themselves from this stress. One protection strategy is based on vertical migrations within the water column or a microbial mats. However, both motility and orientation are impaired by UV radiation. Another means of protection is achieved by the production of screening pigments including mycosporine-like amino acids (MAA) or scytonemins. MAAs are also produced by phytoplankton and macroalgae. In several organisms action spectra were measured which indicate that MAA synthesis is induced by UV in most cases. These sunscreen pigments prevent short wavelength radiation from reaching the UV sensitive DNA where it induces thymine dimers. Remaining dimers are removed by photorepair which involves the enzyme photolyase. The photosynthetic apparatus is another main target in primary aquatic biomass producers. Inhibition of the photosynthetic electron transport chain can be determined by oxygen measurements or by pulse amplitude modulated (PAM) fluorescence. Plants reduce the potentially deleterious effects of solar UV by decreasing the photosynthetic electron transport in photosystem II, a process called photoinhibition. Despite the dramatic effects of even ambient solar UV on individual species and physiological responses, the effect of ozone depletion on whole ecosystems is surprisingly low and close to the noise level induced by all other environmental factors such as mixing layer depth, cloud cover and temperature.