Overfishing is one of the biggest problems of the European Union's common fisheries policy. Overfishing is not only an ecological problem, but also an economic problem for the fishing industry. The problem of overfishing cannot be tackled at the level of the Belgian part of the North Sea alone. Belgian fisheries are in balance with their fishing opportunities. Most important stocks are managed at maximum sustainable yield levels and are considered to be in fairly good condition.

An important aspect of sustainable fisheries is significantly reducing species bycatch to levels that allow species recovery and conservation. By-catches are unintentional catches of non-target species. As the main fishing activities in Belgium consist of demersal fisheries targeting sole and plaice, improving selectivity and reducing by-catches are important objectives. Current fishing gear and practices are being significantly improved to minimise these impacts. In the North Sea, incidental catches in beam trawling mainly concern shark and ray species. Most of these species are protected, live long lives and reproduce slowly. Continuous fishing activities also have an impact on the seabed. In the past, oyster beds, which harboured rich and unique biodiversity, were a precious food source for many other species. However, fishing now prevents these oyster beds from recovering.

The Belgian aquaculture sector is relatively small. In the Belgian part of the North Sea, aquaculture is allowed, under certain conditions, in the two renewable energy zones and in the commercial and industrial zones, all defined by the MSP. The environmental permit for an aquaculture farm is granted on condition that aquaculture reduces the eutrophication of seawater in these zones.