Like the rest of western Washington, San Juan Islands are best visited during the summer. While the sun shines up to 18 hours a day with barely any rain, expect cooler weather compared to the mainland as the surrounding seas cools the warm air. Average summertime temperatures are around 60 °F (16 °C).

The seas however are what makes the island a touch milder in winter than the mainland. The islands can sometimes get lucky enough not to get much rain while the mainland is soaked, thanks to the Olympic Mountains way in the south that blocks the precipitation. The issue that the island faces however, is more with the winds than the rain, where it can sometimes howl and cause problems, especially in the areas exposed to the waters and no surrounding high terrain. These can typically come after a rainstorm or ahead of a dry and chilly weather.

Ferries serve Lopez, San Juan, Shaw and Orcas Islands. For the other islands a private boat or seaplane is required.

From Sidney BC

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	Note: The Sidney-Anacortes ferry service has been suspended and will not resume until at least 2030.
	(Information last updated 01 Mar 2023)

For security and immigration processing when traveling between the US and Canada, a 60-minute advance arrival is strongly suggested for vehicle traffic. Walk on passengers must arrive 30 minutes in advance. Vehicle reservations are recommended. Please speak with Washington State Dept of Transportation Information Agents in Seattle at ☏ +1-888-808-7977 or reserve online. Passports are required to enter either country. Reservations are accepted on the Sidney–Friday Harbor–Anacortes and Anacortes–San Juan Islands routes.

• 2499 Ocean Avenue (Physical), Sidney, BC V8L1T3

• Kenmore Air, toll-free: +1-866-435-9524, fax: +1-425-485-4774, reservations@KenmoreAir.com. Kenmore Air seaplanes make several flights daily from downtown Seattle's Lake Union to six locations in the San Juan Islands with two on San Juan Island, three on Orcas Island, and one destination on Lopez Island. Kenmore Air Express also offers daily land plane service between Seattle's Boeing Field/King County International Airport (BFI ^IATA) and Friday Harbor Airport (FRD ^IATA). Complimentary shuttle transfers are available to/from Seattle-Tacoma International Airport (SEA ^IATA) for passengers on either Kenmore Air service. A quick and spectacular, though not cheap, way to arrive. $75-139. 
• Northwest Seaplanes, 860 W. Perimeter Road, Renton, toll-free: +1-800-690-0086. Scheduled and charter seaplane flights to destinations from South Lake Washington, in the heart of Seattle to the San Juan Islands, Vancouver Island, and British Columbia’s Inside Passage. They operate 4 planes each offering six seats. 

The San Juan Islands are one of the most popular areas for cruising on small craft in North America. Most towns are built around their harbors and offer a variety of services, restaurants, and hotels within walking distance of marinas. Even the less populated islands often have a public dock or public buoys for visiting boaters, check individual island and city listings for specifics. If interested in cruising to the islands, there are charter companies in both Anacortes and Bellingham. The Waggoner Cruising Guide^{[dead link]} is a great resource for these waters.

When arriving from Canada or other foreign countries, there are official U.S. ports-of-entry at Roche Harbor, Friday Harbor, Anacortes and Bellingham that can process boaters through customs. Touch land at a customs dock before any other stops, fines for not doing so can be up to $5000. You will need a passport for everyone on board, your boat's license number, and User Fee Decal number. Customs enforces USDA guidelines for what foods are acceptable to bring into the country. These guidelines are constantly changing so it is best to check in with them before arriving. Boaters are responsible for knowing the prohibited foods and can be fined for not declaring them.

Bringing a car on the ferry is a popular option for exploring the remote areas of the main islands, but car rentals are also available in such areas as Eastsound. Other smaller islands may have unimproved county roads, but due to their remote locations and lack of ferry service these roads often serve as foot trails, and you are more likely to see someone traveling by horse than car. The lines for loading cars onto Washington State Ferries can be notoriously brutal during peak season and weekends. It is not unusual to wait in line for many hours and missing the last ferry can mean a desperate search for unplanned accommodations to spend an unplanned night on the islands so plan accordingly.

The four largest Islands— Orcas, San Juan, Lopez, and Shaw are connected by Washington State Ferries. Water Taxi services can transport to the small islands such as Blakely, Decatur and Henry Islands.

The San Juan Islands are the most popular sailing charter area in the Pacific Northwest and one of the most popular destinations for cruising on small craft in the United States. Small towns and harbors are geared towards visiting boaters and many of the areas most scenic and remote areas can only be reached by boat. The area waters are reasonably protected even in storms off the Pacific, but due to the many underwater hazards some boating experience is helpful. Many charter companies include a day of training in the charter package. See Waggoner Cruising Guide^{[dead link]} for more detailed navigational and recreational information.

The winding paved roads of the main islands are ideal for exploring by bike and bike rentals are available near many areas in the San Juan Islands; however, the smaller more remote islands often do not have paved roads, making traveling by bike more of a challenge. Bicyclists have priority boarding on Washington State Ferries, so bikes can bypass the sometimes ridiculously long car lines and walk right onto the ferries.

Sea kayaking can be a rewarding way to explore the San Juan Islands miles of coastline allowing the paddler a closer and slower look at their surroundings and excellent opportunities to view wildlife, making the San Juan Islands one of the most popular areas to kayak in Puget Sound. Thick forests of majestic pine and deciduous trees and hundreds of creeks and estuaries dot the coastline. Some camping areas in the various state parks in the area are only open to people powered vessels.

Exploring on foot is perhaps the most rewarding way to view the islands. Many trails dot the various islands and state parks giving travelers an insightful view of their surroundings. Outside of the four main islands cars are more of an impractical luxury item rather than a means of transport. Many of the dirt roads see far more foot traffic than car traffic and basically serve as wide foot trails.

Though many of the animals in the Puget Sound area are used to seeing humans, the wildlife is nonetheless wild and should not be fed or disturbed. Be aware of rules for keeping a distance from Orca whales and other marine animals while boating: regulations for killer whales require that boaters stay 200 yards away & keep path of the whales clear. These new U.S. regulations apply to all vessels (with some exceptions) in inland waters of Washington.

Don't disturb resting seal pups, keep children and dogs away and report to the local stranding hotline. Report harassment or sightings of injured/stranded marine mammals by calling the NOAA Fisheries hotline at ☏ +1-800-853-1964>. Seal pups 'haul out' to get much needed rest when they are young and are often alone for many hours. They are extremely vulnerable at this time and should be left alone. Only about 50% of Puget Sound seal pups make it through their first year so please help to protect their health. NOAA recommends at least a 100-yard buffer around seals.

Many visitors are surprised by their monthly phone bills after returning from the San Juan Islands. Due to their close proximity to Canada it is possible to get a better signal from a Canadian cell phone provider and depending on your phone's settings could add foreign roaming charges to your bill. Roche Harbor and north San Juan Island are notorious for having better Canadian service. Check your phone's settings before using and be wary of your cell phone provider's roaming charges. Many of the islands are remote enough that cell phones simply won't work, so don't plan on being dependent on them, especially in the outer islands.

With so many people visiting the San Juan Islands each year petty crimes are something to be vigilant against. Lock your car doors and exercise sensible precautions with valuables, especially when parking your car at a trail head, marina or ferry terminal when you may be away from your car for a while. It would also be advisable to carry anything of value out of sight.