As part of the activities of the Global Ecology and Oceanography of Harmful Algal Blooms (GEOHAB)programme, Open Science Meetings (OSMs) have been organized to discuss and synthesize research efforts on various aspects of harmful algal blooms (HABs), and to plan future collaborative activities relevant to the research theme. Within this framework, the steering committee of the GEOHAB Core Research Project on HABs in Fjords and Coastal Embayments has organized two OSMs. The first OSM was held in 2004 in Santiago, Chile; the major goals were to identify the primary research priorities and to initiate an agenda to further our understanding of HAB dynamics in these small-scale coastal systems. The second OSM was held in May 2012 in Victoria,Canada to highlight the progress accomplished since the first OSM and to focus attention on the importance of a comparative approach in conducting ecosystem studies to improve our understanding of HABs. This second OSM addressed four major themes for which significant advances have been made in recent years, with particular focus on their application to semi-enclosed basins linked to coastal ecosystems: (1) Life history of HAB species; (2) Chemical ecological and toxin interactions; (3) Genetic diversity and (4) Transport and mixing of blooms in small-scale, mesoscale and semi-confined systems. This Report presents the major outcomes of this OSM, followed by recommendations for future collaborative studies. These recommendations include the maintenance of international activities on the ecology and oceanography of HABs after the end of the GEOHAB programme in December 2013. A future agenda should focus on a few key questions with clearly identifiable deliverables. These questions should include the development of (i) improved methods to determine the rates of cyst formation and germination in the field, and (ii) coupled biological-physical-chemical models more appropriate to small-scale environments and which incorporate the role of allelochemicals and toxins, as well as the pelagic and benthic coupling components. Research devoted to life history stages should be continued, particularly with respect to fish-killing algal species that cause particular damage in coastal environments. The influence of aquaculture activities on the development of HABs is poorly understood and should be of greater concern in future research on HABs. The influence of climate change, which may be exacerbated in coastal environments, also should be a focus of future research. Long-term ecological research should be encouraged in this respect, in order to make better predictions in the future concerning the development of HABs in coastal environments.