There are some terrific running options in San Rafael, which is a city of Marin County located in in the North Bay region of San Francisco. Options include attractive shoreline paths and numerous hilly parks and preserves.
San Francisco Bay Trail. A section of the San Francisco Bay Trail runs between Pickleweed Park on San Rafael Creek and Jean & John Starkweather Shoreline Park. There are great views of San Francisco Bay and nearby hills from this paved multi-use path. It’s ~5 flat miles out and back, including a loop around a small lagoon. MAP
China Camp State Park. Gorgeous spot for running, with 15 miles of trails through tidal wetlands, forests, meadows, and grasslands. There are many running options. Best easy-moderate trail is the 7-mile Shoreline/BayView Loop Trail (combine with 0.75 Turtle Back Hill Nature Trail around a pretty marsh). For a challenge, trail runners will enjoy the Bay View/Bay Hills/ Back Ranch Fire Trail to the top of San Pedro Mountain for great views! Most of the trails are fire roads, so they’re wide and have decent footing.