An ecosystem approach means different things to different people. As a result the concept of ecosystem-based fishery management is evolving and it has no universal definition or consistent application. As regards ecosystem modeling, most economic models of fishery ignore the linkages to lower trophic levels. In particular, environmental data and other bottom-up information is widely disregarded. The objective of this paper is to provide a critical review of concepts and ecological economic models relating to ecosystem-based fishery management especially to the environmental issues. The paper started by reviewing basic concepts related to ecosystem-based fishery management and the economic value of ecosystems. Then it aimed to review the development of ecosystem modeling with emphasis on economic aspects of ecology. This was followed by a presentation of the applications of ecosystem-based fishery management in practice. The paper concluded with some critical discussions and brought together conclusions derived from previous literature reviews. We found that although the concept of ecosystem-based fishery management has no universal definition, there is a widespread agreement about the need to implement the ecosystem approach for fisheries in practice. We also revealed that nutrient flow plays a crucial role in an ecosystem. In addition, it has many properties such as recycling and exchanging between consumers and producers, which are similar to monetary flows in an economy. Therefore, nutrients should be chosen as the currency in ecological economic models.