Exposure to harmful algal blooms (HABs) can lead to well recognised acute patterns of illness in humans. The objective of this scoping review was to use an established methodology and the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) reporting framework to map the evidence for associations between marine HABs and observed both acute and chronic human health effects. A systematic and reproducible search of publications from 1985 until May 2019 was conducted using diverse electronic databases. Following de-duplication, 5301 records were identified, of which 380 were included in the final qualitative synthesis. The majority of studies (220; 57.9%) related to Ciguatera Poisoning. Anecdotal and case reports made up the vast majority of study types (242; 63.7%), whereas there were fewer formal epidemiological studies (35; 9.2%). Only four studies related to chronic exposure to HABs. A low proportion of studies reported the use of human specimens for confirmation of the cause of illness (32; 8.4%). This study highlighted gaps in the evidence base including a lack of formal surveillance and epidemiological studies, limited use of toxin measurements in human samples, and a scarcity of studies of chronic exposure. Future research and policy should provide a baseline understanding of the burden of human disease to inform the evaluation of the current and future impacts of climate change and HABs on human health.