Water development has threatened the ecological integrity of riverine ecosystems. Increasing water demand, persistent drought, and climate change exacerbate the effects of habitat degradation and loss in altered systems such as the Colorado River basin. Today, biologists are challenged to identify management actions that benefit native fishes while not hindering water development or management. Herein, we discuss the importance of the natural flow regime for functioning riverine ecosystems and provide examples from four tributaries to the Green River, a major headwater branch of the Colorado River. These tributaries represent a gradient of impacts ranging from water abstraction to the point of complete seasonal desiccation to a relatively natural flow regime, and consequently have maintained different levels of instream habitat complexity and native fish persistence. Despite decades of management, endangered species lack self-sustaining populations and other native species have been extirpated from over half their ranges, which begs the question: can water development and fish conservation be balanced under current water laws and climate change-driven declines in runoff? Given the continued decline in freshwater biodiversity and abundance occurring across the globe, we contend that immediate designation of rivers with natural flow regimes as freshwater conservation areas will enhance native species recovery.