Fisheries and aquaculture are becoming a focus of societal concern driven by globalization and increasing environmental degradation, mainly caused by climate change and marine litter. In response to this problem, the European Atlantic Area NEPTUNUS project aims to support and inform about the sustainability of the seafood sector, boosting the transition towards a circular economy through defining eco-innovation approaches and a steady methodology for eco-labelling products. This timely trans-regional European project proposes key corrective actions for positively influencing resource efficiency by addressing a life cycle thinking and involving all stakeholders in decision-making processes, harnessing the water-energy-seafood nexus. This paper presents inter-related objectives, methodologies and cues to action that will potentially meet these challenges that are aligned with many of the United Nations Sustainable Development Goals and European policy frameworks (e.g., Farm to Fork, European Green Deal).