Fish are some of the most threatened vertebrates in the world due to their often-sensitive response to environmental changes. Major land-use changes in the European Alps have direct and indirect impacts on fish communities, and these impacts are expected to increase in the future. Therefore, the identification of factors that are associated with the distribution of fish communities is of great importance to develop guidelines for management, precautions and sustainable use of running waters. In this study, the relationship of various factors - landscape structure and land use, topography, morphology, hydrology, physical and chemical water characteristics, hormonally active substances, pesticides, food availability, fisheries and piscivores birds - with fish assemblages are analysed. Field data from 81 stream sections from 2001 metres above sea level (m.a.s.l.) down to 219 m.a.s.l. are used in the study. The results reveal that the number of fish species has a strong association with topographic characteristics in the catchment area as well as with landscape configuration. Fish abundance and biomass are associated mostly with land-use type, hydrology, morphology as well as topography. In addition, there are indirect connections between fish abundance and biomass through land-use type, topography, water properties and hydromorphology. The results clearly indicate that not a single factor, but a multitude of factors are associated with the fish communities in the Eastern European Alps.