1. The freshwater pearl mussel (Margaritifera margaritifera) and the thick-shelled river mussel (Unio crassus) are relatively widespread across Europe, but are strongly declining and are now protected by the European Habitats Directive. In the course of this study, 20 pearl mussel and 14 thick-shelled river mussel streams in Bavaria, Germany, were investigated.2. The mussel populations were mapped to determine population size and age structure. For the assessment of habitat quality, host fish abundance and physicochemical parameters were investigated, e.g. substratum quality, water chemistry, redox potential, and turbidity. Furthermore, potential risks for the populations such as predation or river maintenance were also recorded and assessed.3. The average population size and recruitment rates of M. margaritifera populations were lower than in U. crassus populations, with 3517 (2.2% juveniles) compared with 5566 (41.4% juveniles) individuals, respectively. On average, 22.3% of particles were smaller than 0.85 mm in diameter at M. margaritifera sites, whereas the mean proportion of fine particles at U. crassus sites was twice as high, at 41.3%.Other parameters such as redox potential or electric conductivity also indicated more favourable habitat conditions in M. margaritifera streams. Unio crassus seems to be less vulnerable to adverse substratum texture and increased nutrient levels than M. margaritifera.4. The main threats for U. crassus were physical habitat destruction, predation by muskrat, or a lack of host fish, whereas M. margaritifera mainly suffered from siltation leading to a lack of oxygen supply to the interstitial zone, affecting recruitment. Consequently, conservation strategies need to be species-specific and address stream-specific reasons for decline. As a basis, accurate and comparable monitoring data are necessary, which implies the standardization of monitoring protocols.