Fifty-six pharmaceuticals of various chemical groups, such as anti-inflammatory, antibacterial and cardiovascular drugs, were detected in four selected river waters receiving sewage effluents in the Community of Madrid (Spain). A promising approach for the degradation of those residues is the application of a photo-Fenton treatment. Several new bioassays using fern spores were employed for the evaluation of acute and chronic toxicity based on mitochondrial activity, DNA and chlorophyll quantifications of as-received river water and photo-Fenton-treated samples. photo-Fenton treatment provided a high degree of total organic carbon mineralization with up to 70% reduction for river water samples. In addition, the elimination of most of the studied pharmaceutical compounds was confirmed. A few compounds, however (salicylic acid, ofloxacin, caffeine, cotinine and nicotine), seemed more resistant, with after-treatment concentrations between 4 and 44ngL(-1). Nicotine showed the most refractory behaviour with concentrations ranging from 29 to 224ngL(-1) for treated samples. Photo-Fenton treatment yielded a significant decrease in acute and chronic toxicity, even though some residual toxicity remained after treatment. This fact seemed to be related to the presence of toxicants in the water matrix, probably of inorganic nature, rather than the toxic effect of the studied pharmaceutical compounds, as revealed by the effective removal of these compounds and high TOC mineralization of photo-Fenton treatments.