The underwater light climate of a shallow estuary located at the southern coast of the Baltic Sea has been investigated, with special emphasis on the spectral irradiance composition and on short-term irradiance fluctuations caused by vertical mixing and wave focussing. The inherent optical properties of the water body were dominated by phytoplankton pigment absorption in the long-wavelength range and by coloured, dissolved organic matter (cDOM) absorption in the wavelength range <500 nm, including ultraviolet-A (UV-A) and ultraviolet-B radiation (UV-B). Pronounced particulate scattering combined with the absorption values to give very high attenuation coefficients, especially for the shorter wavelengths of UV-B radiation. Photosynthetically active radiation (PAR) was found to be reduced to 1% of the surface value within 0.8 m in the inner, hypertrophic end of the estuary and within 1.9 m in the outer, eutrophic parts of this system, with corresponding 1% penetration depths for UV-B of 0.13 and 0.31 m. During late winter and early spring, the period when reduced atmospheric ozone concentrations and enhanced UV-B have been reported over northern Europe, the irradiance levels in the water column were greatly reduced, due to strong attenuation by ice cover and overlying snow. cDOM concentration of the water was also found to remain at a high level during these periods, and indeed throughout the year, thus reducing the exposure of organisms to UV-R and PAR still further. A complex irradiance regime was found in this system, with irregular and high amplitude fluctuations caused by wind-induced vertical mixing and wave focussing being superimposed upon the solar-angle-dependent seasonal and daily cycles. The methods used to quantify the short-term fluctuations are described, and their relevance to phytoplankton physiology is discussed. The wave-focussing effect is unique to the aquatic environment, and measurements showed that average subsurface irradiances could be increased by up to 5 times for periods lasting for <1 s. The highest irradiances recorded during wave-focussing events reached over 9,000 µmol photons m–2 s–1.