The EU Rapid Alert System for Food and Feed (RASFF) is a tool for the rapid exchange of information on food and feed safety issues between EU member states and the European Commission. It is used to notify food safety authorities about products that pose a risk to human health, including those containing marine and freshwater toxins. Emerging marine and freshwater toxins and their impact on human health and aquatic ecosystems have become a growing concern in the recent years. This is also reflected in the RASFF notifications shared by European countries during the last decade, with the occasional appearance of records relevant to emerging toxins. In this work, RASFF notifications related to emerging marine and freshwater toxins from 2012 to date were retrospectively analyzed, to discover patterns of appearance, as well as explore their relationship with concurrent occurrence data and/or risk assessment advancements in the field. A total of 15 notifications involving emerging marine and freshwater toxins were found, of which ten on ciguatoxins’ presence in fisheries, three on tetrodotoxins in bivalve molluscs (oysters), one on cyanotoxins (microcystins) presence in algae powder and one on pinnatoxins presence in bivalve molluscs (mussels). More than half (6/10) of ciguatera-related notifications were triggered by food poisoning incidents from fishes of the genera Luthanus and Acanthocybium sp. originating from India or Vietnam, whereas the remaining four were connected to border controls on Caranx and Sphyraena sp. fishes imported from India, Sri Lanka and Senegal. All notifications on tetrodotoxins resulted from official market controls conducted in the Netherlands, based on the national measures adopted for tetrodotoxins in 2016. Records on cyanotoxins and pinnatoxins pertained also to official market controls, with the latter based on the risk evaluation of the French Agency for Food, Environmental and Occupational Health & Safety (ANSES) regarding pinnatoxins-associated health risks. The study contributes to better understanding of the main reasons behind RASFF notifications on emerging toxins in E.U. countries and also emphasizes the importance of new occurrence data and relevant risk assessment advancements in the interpretation of the trends observed in RASFF notifications.