Lithologic, magnetostratigraphic, and stable isotope records from the Neogene Xunhua and Linxia basins along the Tibetan Plateau's northeastern margin suggest that topography in the intervening Jishi Shan mountain range began to develop between 16 and 11 Ma. Perturbations to local climate patterns resulting from the evolution of local topography are tracked through comparison of stable isotope compositions of calcareous basin-fill materials across the Jishi Shan. Similarity of isotopic compositions is interpreted to reflect the presence of integrated basins, whereas distinct isotopic compositions reflect unique basin hydrologies. Divergent isotope trends develop between ca. 16 and 11 Ma and are indicative of hydrologic separation in the adjacent Xunhua and Linxia basins and increased aridity in the leeward Xunhua basin. The development of aridity in the lee of the growing topography along the plateau's northeast margin highlights the importance of evaporative enrichment in this extremely continental setting and explains the presence of anomalously positive δ18O values in modern rainfall. Our findings add to a growing body of evidence for deformation along the plateau's north and northeastern margins in the middle to late Miocene.