Increasing agriculture and urbanization inevitably lead to changes in the biodiversity of stream ecosystems. However, few studies examined comprehensively how biodiversity is distributed within and among protected, agricultural and urban land use types in streams. We studied environmental characteristics of streams and patterns of species richness and other community attributes of stream fish communities in these three characteristic land use types in the catchment of the Danube River, Hungary. Land use separated streams to some degree based on their environmental characteristics. However, both between stream environmental and fish community variability were high in most types, and comparable to land use type level differences in case of many streams. A variety of environmental gradients influenced fish community structure rather independently of land use type, which was also influenced by spatial drivers. Non-native fishes modified the structure of native fish communities, especially in agricultural streams, although their modification effect varied more among individual streams than among land use types. In conclusion, land use type proved to be a poor predictor of fish communities in this human modified landscape. We found that even intensively managed areas (i.e. agricultural and urban) can contribute to the maintenance of fish diversity in this biogeographic region, or at least their potential can be comparable to those streams which flow in protected areas. Thus, conservation management should focus on maintaining streams in more natural condition in protected areas and/or use the potential of non-protected agricultural and urban streams in maintaining fish diversity in human modified landscapes.