While other government departments contribute to the management of Canada's water‑based activities, the primary focus of Fisheries and Oceans is on water and the resources it contains. It has responsibility for all matters respecting oceans not by law assigned to any other department. The scope of this responsibility and the extent to which it is exercised by the federal government have been determined by judicial interpretation, agreements with provinces and the evolution of public policy.

Specific responsibilities include:
Provision of programs for the provision of water transportation system and services interests contributing to safe, efficient and economical conduct of marine activities, protection of the marine environment in Canadian waters and, where appropriate, undertaking development, operation and maintenance of specific elements of the marine transportation system.

Scientific research respecting stock assessment and resource conservation requirements, aquaculture regulation and development, primary production, physical oceanography and limnology (studies in freshwater), hydrographic surveying and charting, environmental issues and the behaviour and effects of marine contaminations, and administration of various Federal acts, regulations and policies designed to conserve and protect the aquatic habitat. Assessment and recovery planning for species at risk, and application of an ecosystem approach and integrated management of activities in the oceans.