There is wonderful running in the Berkeley Marina area, about 2 miles west of downtown. A series of three parks and 8+ miles waterside trails along shores, tidal marshes, and beaches, with views out to SF Bay, the Berkeley Yacht Harbor, and South Sailing Basin.
We’ve mapped an 8-mile loop, consisting of the trails around César E. Chávez Park, McLaughlin Eastshore State Park, and Aquatic Park. You can certainly abbreviate the run (I’d leave out Aquatic Park first), or make it longer by running north or south along the Bay Trail.
Good access from University Ave., which is a 2.5 mile straight shot from downtown Berkeley.