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Soda lakes are some of the most productive aquatic ecosystems. 1Krienitz L. The Lesser Flamingo. in: Lesser Flamingos. 2018: 3-18Crossref Google Scholar Their alkaline-saline waters sustain unique phytoplankton communities2Belal E. B. Khalafalla M. M. E. El-Hais A. M. A. Use of spirulina (Arthrospira fusiformis) for promoting growth of Nile Tilapia fingerlings. Afr. J. Microbiol. Res. 2012; 6: 6423-6431https: //doi. org/10. 5897/ajmr12. 288Crossref Google Scholar, 3FAOA review on culture, production and use of Spirulina as food for humans and feeds for domestic animals and fish. FAO Fisheries and Aquaculture Circular. 2008; (No. 1034) Google Scholar and provide vital habitats for highly specialized biodiversity including invertebrates, endemic fish species, and Lesser Flamingos (Phoeniconaias minor). 1Krienitz L. The Lesser Flamingo. in: Lesser Flamingos. 2018: 3-18Crossref Google Scholar, 4Schagerl M. Soda Lakes of East Africa. Springer International Publishing, 2016https: //doi. org/10. 1007/978-3-319-28622-8Crossref Google Scholar More than three-quarters of Lesser Flamingos inhabit the soda lakes of East Africa5Childress B. Nagy S. Hughes B. CMS Technical Series No. 18, AEWA Technical Series No 34. Bonn, Germany2008Google Scholar; however, populations are in decline. 6Birdlife InternationalPhoeniconaias minor. The IUCN Red List of Threatened Species, 2018Google Scholar Declines could be attributed to their highly specialized diet of cyanobacteria7Harper D. M. Childress R. B. Harper M. M. Boar R. R. Hickley P. Mills S. C. Otieno N. Drane T. Vareschi E. Nasirwa O. et al. Aquatic biodiversity and saline lakes: Lake Bogoria National Reserve, Kenya. Hydrobiologia. 2003; 500: 259-276https: //doi. org/10. 1023/A: 1024722821407Crossref Scopus (84) Google Scholar and dependence on a network of soda lake feeding habitats that are highly sensitive to climate fluctuations and catchment degradation. 8Afonina E. Y. Tashlykova N. A. Phytoplankton and zooplankton succession during the dry–refilling cycle: A case study in large, fluctuating soda lakes. Freshw. Biol. 2023; 68: 987-1006https: //doi. org/10. 1111/fwb. 14080Crossref Scopus (1) Google Scholar, 9Schagerl M. Renaut R. W. Dipping into the Soda Lakes of East Africa. in: Soda Lakes of East Africa. 2016: 3-24https: //doi. org/10. 1007/978-3-319-28622-8Crossref Scopus (35) Google Scholar, 10Kirschner A. K. T. Eiler A. Zechmeister T. C. Velimirov B. Herzig A. Mach R. Farnleitner A. H. Extremely productive microbial communities in shallow saline pools respond immediately to changing meteorological conditions. Environmental microbiology. 2002; https: //api. semanticscholar. org/CorpusID: 23727632Crossref PubMed Scopus (16) Google Scholar, 11Felföldi T. Microbial communities of soda lakes and pans in the Carpathian Basin: a review. Akademiai Kiado Rt. 2020; (Preprint at) https: //doi. org/10. 1007/s42977-020-00034-4Crossref Scopus (19) Google Scholar, 12Pellegrinetti T. A. Cotta S. R. Sarmento H. Costa J. S. Delbaje E. Montes C. R. Camargo P. B. Barbiero L. Rezende-Filho A. T. Fiore M. F. Bacterial Communities Along Environmental Gradients in Tropical Soda Lakes. Microb. Ecol. 2023; 85: 892-903https: //doi. org/10. 1007/s00248-022-02086-6Crossref PubMed Scopus (5) Google Scholar 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. 13Ballatore T. J. Bradt S. R. Olaka L. Cózar A. Remote Sensing of African Lakes: A Review. in: Barale V. Gade M. Remote Sensing of the African Seas. Springer, Dordrecht, 2014https: //doi. org/10. 1007/978-94-017-8008-7₂0Crossref Google Scholar 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. 14Girvetz E. Ramirez-Villegas J. Claessens L. Lamanna C. Navarro-Racines C. Nowak A. Thornton P. Rosenstock T. S. Future Climate Projections in Africa: Where Are We Headed? . in: The Climate-Smart Agriculture Papers. 2019Crossref Google Scholar, 15McPhaden M. J. Santoso A. Cai W. El Niño Southern Oscillation in a Changing Climate. American Geophysical Union, 2020https: //doi. org/10. 1002/9781119548164Crossref Google Scholar, 16Cai W. Yang K. Wu L. Huang G. Santoso A. Ng B. Wang G. Yamagata T. Opposite response of strong and moderate positive Indian Ocean Dipole to global warming. Nat. Clim. Chang. 2021; 11: 27-32https: //doi. org/10. 1038/s41558-020-00943-1Crossref Scopus (76) Google Scholar Without improved lake monitoring and catchment management practices, soda lake ecosystems could be pushed beyond their environmental tolerances. 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Byrne et al. (Mon,) studied this question.