The town lies in the Marikina Valley. The Marikina River runs through the western portion of the municipality, while Nangka River runs through the south, bounded by Marikina City. San Mateo has lush trees in other high areas.
The municipality has many spacious parks, tree-lined streets and roads, and industrial zones. Most of the municipality is composed of residential areas, whereas the eastern side is composed of high plateaus and foothills of the Sierra Madre Mountains.