The Whatcom Waterway is located on the Bellingham Bay waterfront in Bellingham, Washington, and is currently managed by the Port of Bellingham (Port). The Whatcom Waterway site includes aquatic areas that have been impacted by contaminants historically released from industrial waterfront activities, including mercury discharges from a former Georgia Pacific (GP) chlor-alkali plant, wood waste and degradation products from historical log rafting activities, and phenolic compounds from pulp mill wastewater discharges, as well as other industrial releases. A remedial investigation/feasibility study (RI/FS) effort was completed in 2007 with the Washington State Department of Ecology (Ecology), and the first phase of cleanup is currently in the final stages of remedial design and permitting. Cleanup activities will be completed in two phases of work. Phase 1 cleanup activities, the focus of this paper, will commence in the summer of 2013 and include structure demolition, shoreline debris removal, shoreline stabilization, new bulkhead construction, remedial dredging, and placement of engineered sediment caps and dredge residuals management cover material. In total, approximately 111,000 cubic yards (85,000 cubic meters) of contaminated sediment and debris will be removed from the Whatcom Waterway during Phase 1 cleanup. This paper discusses key challenges associated with waterfront cleanup at the Whatcom Waterway site, with a focus on the remedial basis of design that was developed to meet cleanup objectives for the project. Specific topics discussed include: integration of cleanup requirements with navigation and existing tenant operational uses; design of shoreline capping and stabilization to meet geotechnical, coastal engineering, and remedial criteria; engineered capping design criteria to accommodate existing and future vessel use; and integration of aquatic habitat mitigation needs. This paper will provide an overview of the complexities associated with a multi-phase cleanup approach at the Whatcom Waterway site, including recontamination potential within the Phase 1 cleanup areas, and coordination with private and public landowners to preserve existing operational site use and account for potential future waterway use changes.