The species-area relationship (SAR) is a well-established, globally recognized ecological pattern, and research on SAR has expanded to include the phylogenetic diversity-area relationship (PDAR). However, this research has generally been limited to terrestrial systems. Using data on freshwater macroinvertebrates, the log–log form of the SAR and PDAR power models were compared between the Lhasa River and the Niyang River on the Tibetan Plateau in China. The study reveals that there is a significant difference in the slopes of SAR and PDAR between the two rivers, with the Lhasa River having a considerably higher slope. The beta diversity calculations in these two basins support this pattern, with the Lhasa River exhibiting significantly higher numbers of species and greater total phylogenetic beta diversity than the Niyang River. Regarding species replacement, the turnover component was the primary driver of both species and phylogenetic beta diversity in both rivers. These differences in the beta diversity components were mainly driven by dispersal constraints because spatial distance had a large effect on total beta diversity and turnover fractions. In addition, the nestedness component was more affected by climate and land cover, indicating that highland rivers are subject to the threats of anthropogenic disturbance and climate change. Therefore, spatial factors play a crucial role in determining the distribution of passively dispersed benthic organisms as the scale of change in rivers increases from local to regional effects.