San Rafael Bay is a broad, open section of the San Francisco Bay system, offering paddlers a mix of sheltered canals and exposed open water. The bay provides scenic views of the San Rafael city skyline, nearby hills, Mount Tamalpais, and the distant San Francisco Bay. The Marin Islands, located within the bay, form a 340-acre national wildlife refuge and support the largest heron and egret rookery in the San Francisco Bay area, making birdwatching a significant attraction. Paddlers will also pass houseboats, docks, and working barges.

Several key public access points serve paddlers. A primary launch is from the San Rafael Canal, where the rental outfitter 101 Surf Sports operates, offering sit-on-top kayaks and stand-up paddleboards. For those with their own craft, Jean & John Starkweather Shoreline Park near the west end of the Richmond-San Rafael Bridge provides a launch with calm water. Loch Lomond Marina features a free carry-in launch area, and McNears Beach Park in a sheltered cove along San Pablo Bay is designated as a San Francisco Bay Area Water Trail trailhead with easy carry-in access. China Camp State Park also offers launch facilities along the shoreline.

The paddling character varies dramatically by location. The San Rafael Canal and other shoreline areas are having calm waters, ideal for beginners. Venturing into the open bay, however, is recommended only for experienced paddlers due to exposure to wind, tides, and boat traffic. Tidal currents are a critical factor, especially around features like The Sisters and Grendel's Needle near Point San Pedro, where water can be dynamic. Paddlers are strongly advised to consult local experts regarding tide and wind conditions before attempting open-water crossings, such as the six-mile round trip to the Marin Islands. North/Northeast winds can create chop and, on some days, provide downwind bumps. The bay experiences a significant tidal range, and paddling during a high slack tide can result in very little current. Major hazards include exposure to direct sun with limited shade, potential sewage spills into the San Rafael Canal as indicated by public warning signs, and sharing waterways with sailboats, superyachts, and dredging equipment. Facilities vary by launch site but can include restrooms, picnic tables, free parking, and nearby markets or restaurants like those at Loch Lomond Marina.