The transitions between the diatoms Aulacoseira spp. ( Melosira ) and the cyanobacteria Anabaena spp. as dominant phytoplankton species in a turbid‐river weir pool are shown to depend directly on the establishment or destruction of persistent thermal stratification. A transition from high to low flow through the pool resulted in the establishment of persistent thermal stratification, causing Aulacoseira to sink out of the euph...