Harmful algal blooms (HABs) increasingly affect Arctic coastal ecosystems, due to hydrographic and bathymetric conditions that support the accumulation of cells and cysts, and coupled with increasing temperatures, extensive bloom events can be easily triggered. However, various harmful algae species have been reported in the past and it is unclear which are most threatening in Greenlandic waters, a region that vitally depend on its fisheries. Here, we explore the diversity and succession of harmful algae by metabarcoding at a multi-year station in Greenlandic coastal waters, offering a comprehensive analysis of species dynamics over time. Dinoflagellates, diatoms and haptophytes, known for their toxin production and potential negative effects on ecosystems and food webs, were regularly detected across years and throughout all sampled months. Yet, results also indicate significant interannual variability in harmful algal occurrences, with high abundances of Alexandrium and increasing abundances of Aureococcus, Prymnesium, and Pseudo-nitzschia. Through a boosted regression tree analysis of the ecological drivers of HABs in Arctic waters, we identified an important role of climate-induced environmental variables such as temperature, salinity, and the number of ice-free days year-1. These findings provide critical baseline data for understanding the future risks of HABs in the Arctic and underscore the importance of ongoing, high-resolution monitoring.