Abstract Studies from Central Europe have shown a relationship between the impaired population status of threatened freshwater mussel species and elevated nitrate nitrogen (N−NO) concentrations in running waters. Causal mechanisms, however, remain unknown, and no experimental data or comprehensive studies involving more species are available, which causes uncertainty in prioritizing conservation actions. This study uses both descriptive and experimental approaches to identify the effects of nitrates on freshwater mussels and demonstrates the need for integrating different research methods for development of conservation strategies for threatened species. Spatial co‐occurrence of five native freshwater mussel species (Anodonta anatina, Pseudanodonta complanata, Unio pictorum, Unio tumidus, Unio crassus) and N−NO concentrations were examined in a 7th‐order river catchment (Lužnice River, Czech Republic) with anthropogenically‐induced increasing N−NO levels and declining populations of these species during the 20th century. Acute toxicity of N−NO was then estimated for artificially reared juveniles of A. anatina and U. crassus using both lethal and sublethal test endpoints. Results showed that the probability of occurrence of all species was significantly reduced in reaches with elevated N−NO levels. In contrast, the results of toxicity testing revealed that the juvenile stages of the two tested species were less sensitive to N−NO than most previously tested freshwater macroinvertebrates. The detected 96‐h median lethal N−NO concentrations were two orders of magnitude higher than the limits derived from distributional data. Despite the probable absence of a direct negative effect of N−NO on freshwater mussel populations, N−NO has potential to be used as an effective indicator of biotope conditions. Identification of causal mechanisms responsible for the observed relationship between unionids and N−NO will require further research. Copyright © 2009 John Wiley & Sons, Ltd.
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