Soda lakes are simple in biodiversity, but due to their highly stochastic environmental dynamics unexpected shifts in species composition do occur. We studied key drivers for structuring phytoplankton communities and identified variables significantly influencing changes of Arthrospira fusiformis abundance in the Kenyan soda lakes, Nakuru and Bogoria. In both lakes, Arthrospira fusiformis dominated algal biomass, but in Nakuru, crashes of this taxon were recorded. The three variables sodium, pH and dry mass significantly contributed to the phytoplankton taxa pattern. Arthrospira was absent at highest turbidity and salinity levels, being outcompeted by the small, single-celled chlorophyte Picocystis salinarium. Picoplankton was in general connected to higher pH values and tended to occur anti-cyclic to Arthrospira. Overall, the abundance of A. fusiformis was influenced by the boundaries of habitat suitability, light penetration, grazers and cyanophages attacks.