Aquatic vegetation (AV) is vital for maintaining the health of lake ecosystems, with submerged aquatic vegetation (SAV) and floating/emergent aquatic vegetation (FEAV) representing clear and shaded states, respectively. However, global SAV and FEAV dynamics are poorly understood due to data scarcity. To address this gap, we developed an innovative AV mapping algorithm and workflow using satellite imagery (1.4 million Landsat images) from 1989 to 2021 and created a global database of AV across 5,587 shallow lakes. Our findings suggest that AV covers 108,186 km2 on average globally, accounting for 28.9% (FEAV, 15.8%; SAV, 13.1%) of the total lake area. Over two decades, we observed a notable transition: SAV decreased by 30.4%, while FEAV increased by 15.6%, leading to a substantial net loss of AV. This global trend indicates a shift from clear to shaded conditions, increasingly progressing toward turbid states dominated by phytoplankton. We found that human-induced eutrophication was the primary driver of change until the early 2010s, after which global warming and rising lake temperatures became the dominant drivers. These trends serve as a warning sign of deteriorating lake health worldwide. With future climate warming and intensified eutrophication, these ongoing trends pose a significant risk of disrupting lake ecosystems.