The Commission is a member of the California Intergovernmental Renewable Energy Task Force, which is planning for future renewable wind and wave energy development opportunities in federal offshore waters along the Pacific Coast. It is also a member of the West Coast Regional Planning Body, a partnership of federally recognized tribes, the states of Washington, Oregon, and California, and federal agencies focused on implementing the U.S. National Ocean Policy.

The Commission partners with the California Natural Resources Agency, Department of Fish and Wildlife, Office of Spill Prevention and Response, California Coastal Commission, State Coastal Conservancy, Department of Parks and Recreation, federal Bureau of Land Management, federal Bureau of Ocean Energy Management, National Oceanic and Atmospheric Administration, and the U.S. Army Corps of Engineers.

The Commission is a member of the California Coastal Commission, San Francisco Bay Conservation and Development Commission, Ocean Protection Council, Delta Protection Commission, Baldwin Hills Conservancy, San Joaquin River Conservancy, and the Lower American River Conservancy. The Commission is a signatory to cooperative interagency agreements, including the agreement for the implementation of the California network of marine protected areas, agreement for the development of the Desert Renewable Energy Conservation Plan, and the San Francisco Bay Materials Management Program. It is also a member of the Marine Protected Area Statewide Leadership Team.

The San Diego Ocean Planning Partnership is a collaborative pilot project between the Commission and the Port of San Diego that centers on public trust uses in the ocean space offshore San Diego County, including commerce, navigation, recreation, fishing, and environmental stewardship. A preliminary assessment report summarizes stakeholder perspectives on how the San Diego ocean space is used, challenges with those uses, and how to approach the ocean planning process. This collaboration also resulted in a web mapping application, an interactive, public-facing, web-based mapping tool that allows the public to view ocean and coastal-related data layers in one place.