Harmful algal blooms (HABs) are natural phenomena that result from the interplay of biological, chemical, physical, and sedimentary processes occurring at different temporal and spatial scales. This paper provides an integrated description of HAB dynamics occurring at the mesoscale (10–100 km, sensu Haury et al., 1978) in confined and semi-confined coastal environments and under stratified water column conditions in a diversity of habitats where HAB events occur. It also focuses on relevant aspects occurring at fine-scale and even smaller cellular scales that are critical to species interactions with their environments. Examples include the key role of life-history stages in the recurrence of HABs in certain embayments; the physical-biological interactions driving the formation, maintenance, and decline of thin layers of plankton, including harmful microalgae; the fascinating, but poorly understood, domain of small-scale chemical interactions between HAB species and components of the food web; the potential link between human activities and climate change; and the trends in HAB occurrence. Development of new observing and sampling technologies and of new modeling approaches has resulted in greater understanding of these phenomena. Two Core Research Projects initiated under the GEOHAB Implementation Strategy, “HABs in Fjords and Coastal Embayments” and “HABs in Stratified Systems,” are discussed and priorities for future research toward improving the management and mitigation of HAB impacts are outlined.