Bivalve aquaculture is worldwide impacted by biofouling development. Immersed infrastructures and shells of the reared species create new substrate for a wide range of epibionts, mainly composed of suspension feeders. Biofouling development is generally considered as a plague for bivalve aquaculture, and its control results in additional costs that can represent up to 30% of total operational costs of the industry. Epibionts have not only consequences for the species they overgrow (i.e. basibiont), but they can also alter the ecological functioning of the exploited ecosystem. In this review, we point out that the assessment of the net effect of biofouling is more complex than expected, as it combines negative and positive effects on both the commercial production and the ecosystem. Furthermore, we emphasize that the removal of biofouling can be stressful and damaging for the reared species. Biofouling control should be carefully reconsidered, on the basis of a holistic approach considering: (i) the interactions between epibionts and their basibionts; (ii) its impact on the final product; and (iii) its contribution to the sustainability of the ecosystem.