Quartermaster Harbor is a sheltered saltwater harbor on the east side of Vashon Island in Puget Sound, formed by Vashon Island to the north and west and land-connected Maury Island to the south and east. It is characterized by calm, protected waters ideal for beginners and families, with a width of about half a mile and a length that supports rewarding sea kayaking adventures of five miles or more. The harbor is shallow, which limits larger marine traffic, though boat traffic is present, especially during events like the major community raft-up and professional fireworks display on July 4th. The north shores feature residences, while the southern shores become more natural with forested hillsides rising from natural beaches.

Primary public access points for paddlers include Burton Acres Park, which hosts a kayak and SUP rental facility, and Dockton Park and Marina on the southern shore. Dockton Park provides a public boat launch, beach access, restrooms, and picnic facilities. Another launch is at Jensen Point. A notable geographical feature is Portage, a narrow isthmus approximately 510 feet wide at high tide connecting Tramp Harbor on the east side of Maury Island to Quartermaster Harbor. This allows paddlers to portage their gear and avoid an eight-mile paddle around the southern tip of Maury Island, shortening the protected route through Quartermaster Harbor to about four miles. Timing this portage for high tide is recommended, as the beaches can dry out far on lower tides, exposing mud.

While the inner harbor is protected, paddlers venturing to the mouth of the bay will encounter more open conditions with views of Mount Rainier. The area is a major wintering spot for over 35 species of birds, and marine life such as shellfish is noted. Paddling is suitable year-round, and guided tours focusing on marine life and island history are available. Key safety considerations include being prepared for immersion with appropriate gear like drysuits, as rescue practices are common, and being aware of increased boat traffic and potential Coast Guard safety inspections during holiday weekends like July 4th. The harbor is also the site of traditional early morning hydroplane races on that holiday.