Management of cyanobacteria has become an increasingly complex venture. Cyanobacteria risks have amplified as society moves forward in an era of accelerated global changes. The cyanobacteria management “pendulum” has progressively shifted from prevention to mitigation, with management considerations often put forth after bloom formation. A universal system (i.e., one-size-fits-all management) fails to provide a management path forward due to the inherent complexities of each lake. A tailored management plan is needed: the right species at the right time in the right place (i.e., the three Rs). The three Rs represent a customizable management strategy that is flexible and informed by advances in scientific understanding to lower cyanobacteria-associated risks. Identifying thresholds in risk tolerance, where thresholds are defined by community collectives, is essential to frame cyanobacteria management targets and to decide on what management interventions are warranted.