Due to the rapid growth of the seafood sector, it is relevant to study the environmental and ecological impacts associated with current and future seafood supply chains of aquatic products aimed for direct or indirect human consumption, including fish, molluscs, crustaceans and algae. Despite efforts, certain challenges remain in seafood LCA. Based on these concerns, this work suggests best practices (including recent methodological developments and novel methods) addressing challenges for the application of LCA to study seafood supply chains, and promoting more holistic and robust outcomes. A literature review was performed, targeting recent reviews, methodological papers, case studies and guidelines for LCAs of seafood-based supply chains. Best practices were identified based on their capacity to complete, complement and support the interpretation of LCAs, their practical demonstration, and our expert judgement. The adoption of these best practices (which address the inclusion of fisheries management concerns, goal and scope decisions, and data availability and management) guarantees solid LCA studies with adequate data and uncertainty management, inclusion of seafood-specific impact categories, and coherent study design.