Aquaculture is increasingly considered a major contributor to the growing demand for worldwide seafood production. Sustainability is becoming a key issue for aquaculture systems, with the objective to produce seafood with lower environmental impacts and that is economically viable and socially fair. In the context of the SIMTAP project, a multi-attribute model called DEXiAqua was developed. DEXiAqua uses the DEX method to assess the sustainability of aquaculture systems via indicators from technical domains and reference methods (i.e., life cycle assessment, life cycle costing, social life cycle assessment, and emergy accounting) selected and organized by the partners in the SIMTAP project. The DEX method consists of building an attribute tree that is organized to characterize a complex problem. Qualitative or quantitative indicators are measured at the end of each branch of the tree. The value of each indicator is translated into a qualitative scale for the associated attribute via threshold values. Weighted utility functions are used to build attributes from sub-attributes until the attribute of overall sustainability is reached. DEXiAqua was applied to a case study of salmon farming in France, which illustrated its ability to assess overall sustainability and help identify ways to improve the production system by identifying environmental, social, and economic hotspots. More case studies are required to apply DEXiAqua to a variety of systems with technical and contextual differences, which could result in changing attribute weights to adapt it better to different contexts.