Harmful (toxic, food web altering, hypoxia generating) cyanobacterial algal blooms (CyanoHABs) are proliferating world-wide due to anthropogenic nutrient enrichment, and they represent a serious threat to the use and sustainability of our freshwater resources. Traditionally, phosphorus (P) input reductions have been prescribed to control CyanoHABs, because P limitation is widespread and some CyanoHABs can fix atmospheric nitrogen (N 2) to satisfy their nitrogen (N) requirements. However, eutrophying systems are increasingly plagued with non N 2 fixing CyanoHABs that are N and P co-limited or even N limited. In many of these systems N loads are increasing faster than P loads. Therefore N and P input constraints are likely needed for long-term CyanoHAB control in such systems. Climatic changes, specifically warming, increased vertical stratification, salinization, and intensification of storms and droughts play additional, interactive roles in modulating CyanoHAB frequency, intensity, geographic distribution and duration. In addition to having to consider reductions in N and P inputs, water quality managers are in dire need of effective tools to break the synergy between nutrient loading and hydrologic regimes made more favorable for CyanoHABs by climate change. The more promising of these tools make affected waters less hospitable for CyanoHABs by 1) altering the hydrology to enhance vertical mixing and/or flushing and 2) decreasing nutrient fluxes from organic rich sediments by physically removing the sediments or capping sediments with clay. Effective future CyanoHAB management approaches must incorporate both N and P loading dynamics within the context of altered thermal and hydrologic regimes associated with climate change. ► Toxic cyanobacterial blooms (CyanoHABs) increasingly threaten global water supplies. ► Human (nutrient) and climate (hydrology, temperature) changes synergistically promote CyanoHABs. ► CyanoHAB control involves reducing both nitrogen and phosphorus inputs. ► Control measures must be adaptive to climatic change.