Harmful Algal Blooms (HAB) are phenomena that result from alterations to ecosystems. Due to their potential toxicity, the level of danger depends on the species concerned, their frequency and intensity. They can cause impacts on biodiversity and on the anthropic activities that take place in maritime and coastal areas. Primary industries such as shellfish fisheries are mainly affected. To deal with this issue, the French administration has built a governance system based on two pillars. The first relies on a water quality monitoring system that assesses the risks of HAB contamination of coastal waters. The second is a regulatory system of production and commercial bans of seafood products from the impacted areas. This public action has two objectives. The first is human health-related and aims to protect consumers of seafood. The second is economic-based and aims to minimize the economic impacts associated with the commercial bans suffered by the businesses concerned. These two objectives may appear to be antagonistic. Using the case study of the French scallop fishery in the eastern Channel and based on an analysis of the commercial bans associated with HAB and associated potential economic impacts, this paper analyses the governance scheme dealing with HAB events in France. The authors highlight that this governance is not only a matter of applying administrative closures when toxicity thresholds are exceeded, but is a dynamic decision-making process involving experts and the Administration that attempts to balance acceptable health risks and economic impacts.