ABSTRACT1. Native freshwater mollusc diversity has been declining over the past decades. For developing efficient conservation management plans for molluscs, it is especially important to identify areas with high native biodiversity.2. The River Danube is one of the most important freshwater ecosystems in Europe and should receive special attention. The main objective of this work was to characterize the composition, diversity and conservation status of freshwater molluscs occurring in the Hungarian Danube River Drainage in five river habitat types (main channel of the Rivers Danube and Tisza, side channels of River Danube, tributaries of Rivers Danube and Tisza).3. In total, 53 mollusc species were identified including 10 invasive species and 12 species of conservation concern. The main determining factors of mollusc composition were sediment characteristics, current velocity and oxygen content. Nitrate-nitrogen, ammonium-nitrogen, and calcium content also play a key role.4. Overall, density, species richness and diversity showed significant differences between habitat types. The highest diversity values were detected in the side channels, but the highest proportion of threatened species was observed in the tributaries. The highest number and proportion of invasive species was detected in the main channel of the Danube. Most of the recorded invasive species were previously documented in side channels and the adjacent wetlands, but did not invade the tributaries.5. Tributaries may provide refuges for native molluscs and could be considered as 'source' populations, which may be critically important in the regional maintenance of threatened species. Tributaries are still less disturbed and less invaded; and should be given priority in future conservation management plans.