It begins near La Mesa Dam as the San Francisco del Monte River, which officially takes the name San Juan River when it meets with Mariblo Creek in Quezon City.

As the San Juan River, it passes through Quezon City, San Juan, the Manila district of Santa Mesa and Santa Ana, and Mandaluyong.

[1][2] Right-of-way issues caused the realignment of the Santa Mesa portion of the Skyway Stage 3.

[2] Culiát Creek, whose headwaters are within the UP Diliman campus, empties into the Pasong Tamó River.

[2][4] The official portion of the river has 9 bridges which are nearly and exactly located at the borders of Quezon City, San Juan, Mandaluyong and Manila.