[5] 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).

The water level and streamflow of the Rio San Jose has been measured at a number of sites in Cibola County, New Mexico.

Stream gauges have been operated by the USGS near Laguna, Correo, and at Acoma Pueblo, near Grants.

[6] Since the 1870s the flow of the upper river has been substantially modified by demands for irrigation, groundwater abstraction and a dam on the Bluewater Creek.