Bertrand Creek
Originating in British Columbia and crossing into the U.S. near the city of Lynden, Bertrand Creek is one of the Nooksack River's largest lowland tributaries. The U.S. portion of the creek is 9.8 miles long, and drains 42.5 square miles, about half of which is in each country.

Canyon Creek
One of the largest tributaries in the Nooksack watershed, Canyon Creek is also one of the most productive spawning grounds for endangered North Fork early chinook. In addition, pink, coho, chum, sockeye, steelhead, and sea-run and resident cutthroat trout also use the creek.

North Fork Nooksack River
The North Fork of the Nooksack River drains 297 square miles, and is the largest fork of the Nooksack. As with the Middle Fork, the North Fork originates from glaciers and snowfields on Mount Baker and Mount Shuksan. It is primarily a forested drainage, with 58% of the land under federal ownership. Most of the 3,871 residents live in the small communities of Kendall, Maple Falls, Glacier, and Welcome. Major tributaries include Racehorse, Kendall, Maple, Boulder, Canyon, Glacier, and Wells Creeks.

Padden Creek
The Padden Creek watershed drains about 3,830 acres on the south end of Bellingham and includes the sub-basins of Lake Padden and Connelly Creek. Throughout the watershed, the elevation ranges from sea level to 985 feet. The upper watershed consists of several unnamed tributaries that flow through forested parks into Lake Padden; the lower portion is drained by Padden Creek as it meanders 2.9 miles from Lake Padden to Bellingham Bay, through residential development and city parks. The area includes moderate density residential use, forested parks, a golf course, a commercial garden and a retail area.

Mainstem Nooksack River
The Mainstem Nooksack River lies downstream of the three forks: the North Fork, Middle Fork, and South Fork. From the confluence of the Middle and North Fork, the mainstem flows 36 miles through low lying agricultural and rural areas, as well as, the communities of Deming, North Cedarville, Nooksack, Everson, Lynden, Ferndale, and the Lummi Nation before discharging into Bellingham Bay. Many major tributaries of the mainstem form sub-basin watersheds throughout Northern Whatcom County and portions of Canada. For inventory purposes, the Mainstem Nooksack River may also be viewed as a sub-basin that includes an area where ground and surface water directly drain into the mainstem or its minor tributaries. The tributaries included in this sub-basin are Anderson Creek, Smith Creek, McCauley Creek, Cougar Creek, Scott Ditch, Schneider Ditch and Wiser Lake.

Birch Bay
The Birch Bay Watershed encompasses 20,173 acres of land along the shores of northwestern Whatcom County. It includes Fingalson Creek, Terrell Creek, Lake Terrell, and several other small tributaries, which drain into Birch Bay, an inlet of Georgia Strait. A large portion of the watershed consists of agricultural land (6,507 acres) and natural areas (6,953 acres). The remaining portions of the watershed support residential, commercial, and industrial land uses.

Bellingham Bay
With a population of over 57,000, Bellingham Bay is a primarily urban drainage. It encompasses the smaller drainages of Whatcom, Padden and Chuckanut Creeks, as well as Fragrance and Padden Lakes. Most of the Bellingham Bay watershed is zoned for urban uses, with rural, forestry, open space, and commercial/industrial uses making up the balance. (For purposes of WRIA watershed and salmon planning, Lake Whatcom and Squalicum Creek are considered to be separate watersheds from Bellingham Bay.)

Squalicum Creek
One of the largest independent drainages in Whatcom County, the Squalicum Creek watershed includes most of northern Bellingham, beginning at Squalicum and Toad lakes and stretching west to Bellingham Bay. Encompassing 24 square miles (15,097 acres), the watershed encompasses Baker Creek, which joins Squalicum near Meridian Street and is the largest of the tributaries, as well as Spring and McCormick creeks. In addition, Squalicum Creek flows through Sunset Pond and Bug Lake, two “borrow pits” used to provide fill during the construction of I-5.

Middle Fork Nooksack River
Draining 103 square miles, the Middle Fork Nooksack subbasin is located in the western portion of Whatcom County. The headwaters of this watershed begin at an elevation of 10,778 feet atop the Deming Glacier, on the south face of Mount Baker. Flowing northwesterly for 16 miles, the Middle Fork Nooksack reaches its lowest elevation of 290 feet at its confluence with the North Fork Nooksack River, just east of Deming.

Ten Mile Creek
The Tenmile Creek watershed, which includes both Nooksack lowlands and the King Mountain uplands, is located in the central part of Whatcom County. It encompasses 65 miles of creeks and streams throughout 35 square miles (22, 670 acres), and includes Tenmile, Fourmile, and Deer creeks, as well as Crystal Springs, Barrett, Green and Fazon lakes. Over 50% of the watershed is used for agriculture, testimony to the fertile alluvial soils of the lowlands.

South Fork Nooksack River
The South Fork Nooksack drains an area of 184 square miles from its headwaters on the eastern flanks of the Twin Sisters Range to its confluence with the mainstem Nooksack River near Deming. Along the way, the main channel of the South Fork covers more than 40 miles in Whatcom and Skagit counties, with many more stream miles traveled by its numerous tributaries, such as Cavanaugh, Skookum, Hutchinson, and Jones creeks. Typically, the tributaries originate in steep headwater areas, with numerous cascades and waterfalls found in the uppermost reaches. Downstream, the tributaries enter the floodplain of the South Fork as it winds its way through the valley floor, providing accessible habitat for salmon spawning and rearing.