The paper discusses the development of scientific basis of marine natural resource use. The authors believe that rational marine environmental management requires an adequate understanding of features that reflect changes in the functioning of marine ecosystems under changing natural conditions and the growing pressure of anthropogenic impacts. A fundamental understanding of the phenomena and processes occurring in the seas and oceans is necessary for the transition to such marine use. The authors try to answer the following questions: what is the main object of management in marine use; what is the integrated management of the marine ecosystem; what is the essence of the ecosystem approach in marine use; what is the range of tools included in the economic component of rational marine use. The analysis carried out in the article allowed the authors to formulate the most promising tools for ensuring sustainable and environmentally safe development of the marine economy. It includes: integrated management of marine activities using an ecosystem approach, marine spatial planning, application of a precautionary approach in planning marine activities aimed at reducing environmental risks in areas of extreme climatic conditions, assessment of marine ecosystem services in the system of management decisions in marine use. The authors conclude that the improvement of these tools should be the goal of scientific research to create a theory of marine environmental management.