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The implementation of the Lake Whatcom Management Program is guided by five-year work plans that are organized around twelve program areas. Introductions to the twelve program areas can be found in this section.
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 The Land Preservation Program Area aims to reduce water quality impacts to Lake Whatcom by preserving land within the watershed that might otherwise be made available for development.
 The Stormwater Management Program Area aims to prevent water quality and quantity impacts associated with stormwater runoff.
The Urbanization and Land Development Program Area aims to reduce water quality impacts resulting from residential and land use development activities.
The Community Outreach Program Area aims to protect water quality by encouraging watershed residents and visitors to become stewards of the lake.
The Data and Information Management Program Area aims to collect and manage data to increase our understanding of water quality, pollution source, and land use trends over time and to guide management decisions accordingly.
The Spill Response and Hazardous Materials Program Area aims to prevent water quality impacts associated with improper storage and handling of hazardous materials within the watershed and to ensure that spill prevention and response programs adequately protect water quality.
The Forestry/Fish/Wildlife Program Area aims to protect the clean water functions provided by forests located in the Lake Whatcom watershed.
The Transportation Program Area aims to limit transportation-related impacts to water quality by encouraging watershed residents to use alternative transport and to limit the number of vehicle mile trips being made in the watershed.
The Recreation Program Area focuses on promoting recreational opportunities that minimize impacts to water quality while reducing the impacts of existing recreational activities.
The Utilities and Waste Management Program Area aims to promote water-use efficiency by residential, industrial, and commercial users. This program area also strives to minimize water quality impacts associated with on-site waste systems.
The Administration Program Area aims to effectively administer and coordinate the Interjurisdictional Coordinating Team (ICT) and Program Area Committee activities to support the successful implementation of the Lake Whatcom Management Plan.
The Enforcement Program Area aims to support enforcement of land use, development and other associated regulations to protect the water quality of Lake Whatcom.