Water managers worldwide are facing the serious problem of dense blooms of cyanobacteria in surface waters. In the quest for the optimal method to combat cyanobacterial dominance, many questions and many possible solutions arise. This paper presents a three-phase strategy to fight harmful cyanobacterial proliferation. Water managers who apply this strategy can generate a tailor-made set of measures. The three phases consist of (1) defining the ecological water quality targets of the waterbody in question, (2) assessing its current ecological state, and (3) selecting which measures will yield optimal results. The paper provides assistance in the quantitative diagnosis of the state of both shallow and deep temperate freshwater lakes by means of a lake system analysis, and presents a survey of measures. Measures are divided into two sets. Preventive measures are based on switching to a clear state (shallow lake) or reducing the overall cyanobacterial biomass (deep lake). They are subdivided into nutrient reduction, hydromorphological adjustments, and food web management. Concerning nutrient reduction, in many situations phosphorus management alone should suffice. Nitrogen management can be important to increase the species diversity of macrophytes, or to relieve downstream (marine) consequences. Control measures (including mitigation) have a direct impact on cyanobacterial blooms by biomass removal, flushing, or mixing; however, the number of proven technologies is limited.