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Soda lakes are some of the most productive aquatic ecosystems. 1 Their alkaline-saline waters sustain unique phytoplankton communities 2,3 and provide vital habitats for highly specialized biodiversity including invertebrates, endemic fish species, and Lesser Flamingos (Phoeniconaias minor). 1,4 More than three-quarters of Lesser Flamingos inhabit the soda lakes of East Africa 5 ; however, populations are in decline. 6 Declines could be attributed to their highly specialized diet of cyanobacteria 7 and dependence on a network of soda lake feeding habitats that are highly sensitive to climate fluctuations and catchment degradation. 8,9,10,11,12 However, changing habitat availability has not been assessed due to a lack of in situ water quality and hydrology data and the irregular monitoring of these waterbodies. 13 Here, we combine satellite Earth observations and Lesser Flamingo abundance observations to quantify spatial and temporal trends in productivity and ecosystem health over multiple decades at 22 soda lakes across East Africa. We found that Lesser Flamingo distributions are best explained by phytoplankton biomass, an indicator of food availability. However, timeseries analyses revealed significant declines in phytoplankton biomass from 1999 to 2022, most likely driven by substantial rises in lake water levels. Declining productivity has reduced the availability of healthy soda lake ecosystems, most notably in equatorial Kenya and northern Tanzania. Our results highlight the increasing vulnerability of Lesser Flamingos and other soda lake biodiversity in East Africa, particularly with increased rainfall predicted under climate change. 14,15,16 Without improved lake monitoring and catchment management practices, soda lake ecosystems could be pushed beyond their environmental tolerances. [Display omitted] • Lesser Flamingo distributions are determined by lake productivity and water levels • Productivity has declined across East African soda lakes due to rising water levels • Flamingo distributions will likely shift north and south away from the equator • Declines in healthy soda lake ecosystems threaten their unique biodiversity More than three-quarters of the world's Lesser Flamingos feed on the cyanobacterial blooms present in the productive soda lakes of East Africa. Byrne et al. show that rising water levels are driving significant declines in soda lake productivity, reducing the habitat availability for Lesser Flamingos and other soda lake biodiversity. [ABSTRACT FROM AUTHOR]