Muggelsee is a shallow lake in the suburban region of Berlin, Germany and included in the lake-river system of the river Spree, having an average annual retention time of 42 days which increases to > 100 days in the summer period. The summer equilibrium phase of phytoplankton results in the development of an Aphanizomenon flos-aquae dominated assemblage which, in some years, progresses towards a Microcystis dominated assemblage. Continuously high flushing (in range of 1%-2% of lake volume day (-1) does not prevent Aphanizomenon development but its biomass remains at low levels as compared to other summers with smaller average flushing. In such years (flushing remains < 1% of lake volume day (-1)) a flushing pulse of 1%-2% of lake volume day (-1) has been effectual to break development of cyanoprokaryotes and to decrease their biomass to low levels. The major reason of the decrease is not the dilution effect of flushing pulses but the intolerance of cyanoprokaryotes to sudden environmental changes. Considering the case of Muggelsee from the point of view of reservoir ecology it can be concluded that reservoirs with pulsed use are less exposed to development of cyanoprokaryotes if pulses occur in a sufficient frequency (20-30 days) and their intensity falls to the range of 1%-2% of reservoir volume day(-1). Reservoirs with continuous take off of water are more exposed to cyanoprokaryota development with all the consequences for water use.