Anthropogenic nutrient overenrichment, coupled with rising temperatures, and an increasing frequency of extreme hydrologic events (storms and droughts) are accelerating eutrophication and promoting the expansion of harmful algal blooms (HABs) across the freshwater-to-marine continuum. All HABs—with a focus here on cyanobacterial blooms—pose serious consequences for water supplies, fisheries, recreational uses, tourism, and property values. As nutrient loads grow in watersheds, they begin to compound the effects of legacy stores. This has led to a paradigm shift in our understanding of how nutrients control eutrophication and blooms. Phosphorus (P) reductions have been traditionally prescribed exclusively for freshwater systems, while nitrogen (N) reductions were mainly stressed for brackish and coastal waters. However, because most systems are hydrologically interconnected, single nutrient (e.g., P only) reductions upstream may not necessarily reduce HAB impacts downstream. Reducing both N and P inputs is the only viable nutrient management solution for long-term control of HABs along the continuum. This article highlights where paired physical, chemical, or biological controls may improve beneficial uses in the short term, and offers management strategies that should be enacted across watershed scales to combat the global expansion of HABs across geographically broad freshwater-to-marine continua.