Climate change is increasing the severity and extent of extreme droughts events, posing a critical threat to freshwater ecosystems, particularly with increasing human demands for diminishing water supplies. Despite the importance of drought as a significant driver of ecological and evolutionary dynamics, current understanding of drought consequences for freshwater biodiversity is very limited. We describe key barriers that hinder integrative drought research and monitoring across riverscapes. The primary constraint limiting understanding of ecological drought is an existing monitoring framework focused on human water consumption and flood risk in mainstem rivers. This approach is misaligned with escalating needs for research and data collection that illuminate exposure, sensitivity, and adaptive capacity (i.e., vulnerability) of biota to drought across entire riverscapes. We present a hierarchical framework for integrated ecological drought monitoring and research that addresses drought vulnerability across riverscapes, and describe how this approach can directly inform natural-resource management.