Critical aspects of the environment can reduce the efficiency of Environmental Management Systems (EMS) when applied to Marine Transport. Accordingly, this paper focuses on the improvement of the traditional EMS approach through the usage of Balanced Scorecard (BSC). The BSC represents a managing tool able to measure and increase organizational performance, taking into consideration environmental aspects. The proposed method, based on the ISO 14001 standard, allows management of environmental metrics through conventional BSC systems and it is applied to the biggest organization for marine transport in Montenegro as a case study methodology. In this qualitative investigation, particular attention was paid to creating EMS criteria able to orient the complete business operation of the organization but also to test their potential linkage to the conventional BSC approach. Four models of the BSC were created, each one including to a different extent the issue of environmental protection. Finally, an expert’s evaluation of model efficiency, based on the ISO 9126, was carried out. As a result, the best ranked model is recommended for the selection of an approach toward environmental protection based on the use of the EMS metric in a conventional BSC system. This method—in short ECO-BSC—was developed for the specific benefit of those organizations operating on the marine transport market.