The Rio San Jose's farthest tributary stream is
Bluewater Creek; its headwaters are in the
Zuni Mountains, near the
continental divide in
Cibola County, with about 400 feet of the course in
McKinley County. Bluewater Creek is dammed to form
Bluewater Lake, with a capacity of . The Rio San Jose proper starts at the confluence of Bluewater Creek and Mitchell Draw near
Bluewater Village. Entering
Valencia County, it flows southeast, through
Grants, then turning east near
McCartys, flowing through the
Acoma Indian Reservation and
Laguna Pueblo. The remains of an ancient dam constructed by the Laguna people sometime between 1370–1750 AD is situated within Laguna Pueblo. Below
Mesita the river turns southeast again, flowing through a narrow canyon before joining the
Rio Puerco in
Bernalillo County. The entire course of the river below Bluewater Creek is roughly paralleled by the
BNSF Railway tracks (formerly the
Atlantic and Pacific Railroad, built around 1882, later absorbed into the
AT&SF). Between Bluewater Village and Mesita the river valley provides the route for old
U.S. Route 66 and
I-40. ==Hydrology==