The ongoing global environmental change poses a serious threat to rivers. Comprehensive knowledge of how stressors affect biota is critical for supporting effective management and conservation strategies. We evaluated the major gradients influencing spatial variability of freshwater biodiversity in continental Spain using landscape-scale variables representing climate, land use and land cover (LULC), flow regime, geology, topography, and diatom (n = 117), macroinvertebrate (n = 441), and fish (n = 264) communities surveyed in minimally impacted streams. Redundancy analysis identified the environmental factors significantly contributing to community variability, and specific multivariate analyses (RLQ method) were used to assess trait–environment associations. Environmental variables defined the major community change gradients (e.g., mountain–lowland). Siliceous, steep streams with increased precipitation levels favored stalked diatoms, macroinvertebrates with aquatic passive dissemination, and migrating fish. These traits were replaced by adnate diatoms, small macroinvertebrates, and non-migratory fish in lowland streams with warmer climates, calcareous geology, agriculture, and stable flow regimes. Overall, landscape-scale environmental variables better explained fish than diatom and macroinvertebrate community variability, suggesting that these latter communities might be more related to local-scale characteristics (e.g., microhabitat structure, substrate, and water physicochemistry). The upslope environmental gradient of river networks (e.g., slope, temperature, and LULC changes) was paralleled to the observed taxonomy-based and trait-based spatial variability. This result indicates that global change effects on riverine biodiversity could emerge as longitudinal distribution changes within river networks. Implementing management actions focusing simultaneously on water temperature, hydrological regime conservation (e.g., addressing LULC changes), and river continuity might be the best strategy for mitigating global change effects on river biodiversity.