Rivers are among the most threatened ecosystems worldwide, with their biodiversity facing pressures from both natural variability and human activities. Compared to river ecosystems in humid regions, those in semi-arid regions are more fragile and susceptible to environmental stresses. However, the impacts of diverse environmental stresses on multiple facets of riverine phytoplankton beta diversity in semi-arid basins remain understudied. Here, we examined the responses of taxonomic (T(3), functional (F(3), and phylogenetic (P(3) beta diversity of riverine phytoplankton communities to land use, water quality, bioclimate, and spatial structure in the middle reaches of the Yellow River Basin in Northwest China. Field surveys were conducted across 33 rivers in three distinct geomorphic regions during autumn (2022) and spring (2023), respectively. We identified a total of 367 phytoplankton taxa representing 127 genera and 7 phyla in samples collected from the Loess Plateau (LP, north), Guanzhong Plain (GZ, middle), and Qinling Mountains (QL, south). Bacillariophyta (40 %) and Chlorophyta (30 %) were dominant across regions during both seasons. Phytoplankton richness and density were higher in spring than in autumn and increased from QL to GZ and LP. T(3 (79.8 %) and P(3 (62.8 %) were mainly driven by turnover, with F(3 (72.6 %) dominated by nestedness. F(3 trended downward from south to north across the QL, GZ and LP regions. The major ecological processes influencing phytoplankton beta diversity displayed seasonal variation, represented by dispersal limitation in autumn and environmental filtering in spring. These findings present a holistic picture of riverine phytoplankton beta diversity within a large-scale semi-arid basin, and recommendations are proposed for the management and conservation of aquatic ecosystems.