Padden Creek meanders from Lake Padden to Bellingham Bay, ending its 2.8-mile journey at the estuary located between Harris Avenue and the train trestle.  The watershed serves a 6-square-mile area, providing drainage for Old Fairhaven, Western Washington University and four public schools.  Other "customers" include the parks at Fairhaven, Happy Valley and Lake Padden, as well as Connelly Creek Nature Area.  Connelly Creek is Padden Creek's largest tributary.

Padden Creek is home to Coho, Chinook, Chum and Steelhead, as well as resident and sea-run Cutthroat Trout.  The estuary supplies food and shelter for salmon and shorebirds, and affords a transition between the fresh and saltwater environments.  Most of the Padden Creek estuary has been filled in and is now only one-tenth of its original size.

Nearly one-half mile of the creek was buried in a culvert in 1892.  Efforts are underway to establish a new channel above ground to improve fish habitat and control flooding.