Spatial patterns in bird community structure are closely related to changes in habitat composition at small spatial scales, but the explanatory power of habitat declines towards larger scales, where dispersal limitations and historical factors becoming more important. To disentangle these effects, we performed a large-scale bird census using a small-scale field approach in the Czech Republic. Using canonical correspondence analysis, we found that the strongest scale-independent gradient in bird community composition goes from higher-altitude forest assemblages to lower-altitude farmland and human settlement assemblages. The other gradients were also scale-dependent, probably due to the different distributional patterns of particular habitats at the respective scales. Closer examination of bird occurrence in particular habitats revealed that water bodies host the most distinct bird assemblage compared to the assemblages of other habitats. Interestingly, although the census tracked the most important east-west biogeographical gradient within the Czech bird fauna, we did not find longitude to be a significant predictor of changes in bird community structure along the transect at any resolution. We suggest that the biogeographical gradient is actually related to the habitat-based distinction between the coniferous-forested higher-altitude West and the deciduous-forested lower-altitude agricultural East. Fine-scale bird-habitat associations are thus responsible for the patterns of community structure at all spatial scales.