Reservoir sedimentation is an escalating threat to global water security. While most existing assessments focus on large, well-managed reservoirs, they overlook the vast and vulnerable network of smaller reservoirs, which hampers our understanding of global sedimentation risks. Here we present a high-resolution global assessment of reservoir sedimentation in over 550,000 reservoirs, similar to 95% of which are <1 km(2), based on a physics-guided machine learning model and a comprehensive reservoir inventory. Sedimentation rates have been underestimated in over 75% of reservoir-bearing regions when large reservoirs alone are considered. This oversight conceals a loss in global average reservoir water storage of 7.3% +/- 2.8% per decade, with nearly one in five reservoirs now facing high-risk status. We identify 16 global high-sedimentation hotspots across the Western Americas and Afro-Eurasian Sediment Belts, threatening water supplies to over 2 billion people and impacting similar to 26% of global irrigated land. Without intervention, we project that, by 2060, more than half of all reservoirs could become functionally inoperable, including 58.6% of small and 38.1% of large reservoirs. These findings highlight an urgent need for targeted, nature-based sediment management, particularly in dryland regions, where small reservoirs are critical for domestic water access and food production.