At first glance, the oceans and lakes that sustain us appear vast, steady, and predictable. Yet beneath their shimmering surfaces, microscopic life has long engaged in chemical warfare—quiet, invisible, and often devastating. Phycotoxins, the potent molecules produced by microalgae and cyanobacteria, are the weapons of an ancient conflict. Far from being biological curiosities, they shape who lives, who dies, and how aquatic ecosystems function. Only in recent decades have we begun to grasp the scale and sophistication of this chemical arsenal, and the consequences of its release into the waters we depend on. Within this chapter, we invite the reader into the dynamic world of harmful algal blooms (HABs)—events in which normally inconspicuous microorganisms erupt into dense, toxin-producing swarms that can alter entire ecosystems. We explore how algae manufacture an extraordinary diversity of bioactive compounds: neurotoxins that silence nerve impulses in milliseconds, hepatotoxins that disrupt liver cells, and allelopathic metabolites that sabotage competitors with surgical precision. These molecules, honed over millions of years, reveal algae not merely as passive drifters but as active, strategic players in ecological competition. But the story doesn’t end at the microscopic level. Increasingly, it is clear that we humans are creating the very conditions in which toxic algal blooms thrive. Warming waters, nutrient pollution, altered hydrology, and globalization are driving HABs to become more frequent, more disruptive, and more unpredictable than ever before. What is often portrayed as a “natural phenomenon” is, in fact, a symptom of global changes that we are actively shaping. The consequences extend far beyond ecological disruption: coastal economies falter, fisheries and aquaculture are threatened, drinking water systems become contaminated, and entire communities lose trust in the waters that once provided food, income, and recreation. Amid these challenges, we also encounter the remarkable ways animals—from zooplankton to fish, birds, and even marine mammals—cope with algal xenobiotics. Some have evolved biochemical shields, detoxification pathways, or behavioral strategies that allow them to survive in toxin-laden environments; others succumb, triggering cascading ecological consequences. By weaving together insights from chemistry, ecology, evolution, and environmental change, this chapter provides a panoramic introduction to the world of phycotoxins and harmful algae. It offers not only a foundation for understanding the science behind these phenomena but also a compelling narrative of how ancient molecular strategies are colliding with modern human pressures to reshape aquatic ecosystems worldwide. It is a story that is still unfolding—one whose urgency, complexity, and fascination make it essential reading for scientists, students, and anyone concerned about the future of our planet’s waters.