Vast hydropower resources are still untapped, particularly in the world’s emerging economies, deployment of which could provide energy-economic benefits but also affect riverine ecosystems. It is unclear how rapid economic growth and transition to low-carbon energy may impact hydropower development, with potential countervailing effects of increasingly cost-competitive variable renewable energy (VRE). Using the Global Change Analysis Model (GCAM), an integrated model of global energy-water-economy dynamics, we explore the effects of these forces on hydropower expansion in the world's 20 most eco-sensitive river basins, that have high untapped hydropower potential and ecological richness. We find that a transition to low-carbon technologies exerts the strongest development pressure, causing over 80% deployment of exploitable potential in more than 72% of the eco-sensitive basins by 2050, while rapid economic growth causes such deployment in 44% of the basins. Enhanced integration of VRE helps reduce deployment levels, which mostly alleviates the hydro deployment associated with rapid economic growth, but not that from the low-carbon transition. Our results also show large uncertainties in the level of mid-century deployment in several basins, including the Ganges, Amazon, Nile, and Mekong -- indicating opportunities to explore strategic planning and alternative techniques aimed at balancing tradeoffs between sustainable development objectives, including clean energy and the health of freshwater ecosystems.