Drying alters the structure and dynamics of riverine communities by filtering sensitive taxa locally and isolating populations along fragmented river networks. Although ecological theory suggests that consequences of drying should depend on location (headwaters vs. mainstem reaches), limited research has examined variation in drying patterns across geographies–or how these patterns affect riverine biodiversity. Here, we examined: (i) variability in spatial patterns of drying across U.S. climates and geographies; (ii) how drying controls community diversity through local disturbance, network-wide fragmentation, and drying location; and (iii) whether the relationship between drying location and community diversity is contingent on climate. To this end, we examined over 15,000 watersheds across the U.S. and quantified associations between reach-level drying probability and reach location within the river network. We then simulated river networks that dry predominantly in headwaters, in lower reaches, or randomly; and used a mechanistic model to simulate metacommunity dynamics across drying structures, fragmentation levels, and disturbance severities. We found high variation in the spatial structure of drying in nature, with most Eastern U.S. watersheds showing upstream-biased drying or perennial conditions; and most in the Western U.S. drying in mainstems or throughout the network. Further, we found an association between maximum seasonal aridity and mainstem drying. The metacommunity simulations showed a synergistic interaction between local disturbance and network-level fragmentation on community diversity, with spatial drying patterns altering both the effects of fragmentation and local disturbance. Notably, mainstem-biased drying uniquely reduced alpha diversity across all connectivity levels. Finally, empirical sampling of stream invertebrates in ten intermittent watersheds across the U.S., spanning from mesic to arid climates, showed high congruence with model simulations. Our work shows that downstream-biased drying is particularly harmful to riverine communities, suggesting that aridity and human activities that dewater river mainstems are poised to erode riverine biodiversity in previously-overlooked ways.