Distribution patterns of epilithic diatom assemblages in streams in northeastern Spain and their relation to different environmental gradients are presented. Thirty-five sites were sampled covering a wide range of fluvial typologies. Gradient analysis was used to analyze the community structure and the major ecological gradients underlying variation in species composition. Two major gradients were evident; the first was a complex gradient from oligotrophic, pristine, fast-flowing highland rivers to mainly eutrophic rivers of low elevation; and the second related to altitudinal and seasonal variation of temperature. Two sets of factors were evident; one was associated with water chemistry, and the other to seasonal and physiographical variation. Variance partitioning allowed the separation of the effects of the different sets of environmental parameters. The contribution of physiography and water chemistry to diatom distribution was more unclear when the level of disturbance was intermediate. Considering the relatively high proportion of variation explained by physiographical variables alone, we suggest that when using diatoms to evaluate water quality, ecoregional characteristics of river stretches should also be considered.