The Whatcom County Council is the legislative branch of Whatcom County government. It is comprised of 7 members, one elected from each of the 5 County Council districts, and 2 elected as the countywide at-large representatives. The County Council exercises its legislative power by adoption and enactment of ordinances and resolutions. The entire County Council acts as: The Committee of the Whole, to hear items that must be discussed in closed executive session; The Whatcom County Board of Health, in all matters pertaining to the preservation of life and health of people within Whatcom County; The Whatcom County Flood Control Zone District Board of Supervisors, to approve projects for the Flood Control Maintenance Program.

The Council has 5 committees: Finance and Administrative Services Committee: budget, taxation and purchasing, personnel policies and union negotiations; Natural Resources Committee: water, forestry, agriculture, fishery, and mineral issues; Planning and Development Committee: zoning, development, stormwater, fire, and septic and sewer issues; Public Works and Health Committee: road construction and vacation, new construction, remodeling, public utility issues, and criminal justice issues; Criminal Justice and Public Safety Committee: criminal justice activities and planning, public safety, and law enforcement.