Connectivity between fluvial and aeolian sedimentary systems plays an important role in the physical and biological environment of dryland regions. This study examines the coupling between fluvial sand deposits and aeolian dune fields in bedrock canyons of the arid to semiarid Colorado River corridor, southwestern USA. By quantifying significant differences between aeolian landscapes with and without modern fluvial sediment sources, this work demonstrates for the first time that the flow- and sediment-limiting effects of dam operations affect sedimentary processes and ecosystems in aeolian landscapes above the fluvial high water line. Dune fields decoupled from fluvial sand supply have more ground cover (biologic crust and vegetation) and less aeolian sand transport than do dune fields that remain coupled to modern fluvial sand supply. The proportion of active aeolian sand area also is substantially lower in a heavily regulated river reach (Marble–Grand Canyon, Arizona) than in a much less regulated reach with otherwise similar environmental conditions (Cataract Canyon, Utah). The interconnections shown here among river flow and sediment, aeolian sand transport, and biologic communities in aeolian dunes demonstrate a newly recognized means by which anthropogenic influence alters dryland environments. Because fluvial–aeolian coupling is common globally, it is likely that similar sediment-transport connectivity and interaction with upland ecosystems are important in other dryland regions to a greater degree than has been recognized previously.