Topography and Land Management Units.
The topography of San Rafael is defined by being sandwiched between two rivers: by the Angat River in the southern boundary with the Municipality of Baliwag and Maasim River along the northern boundary with the Municipality of San Ildefonso. The topography is further defined by the level plains in the western section and the undulating to hilly mountains on the eastern section. A pronounced topographic feature is the abandoned railroad track that runs from south to north almost separating the warm cool lowlands in the western side from the warm cool uplands in the eastern side. West of the railroad track are the plains while the undulating to hilly mountains can be found on the east of the railroad track. The eastern section of the municipality is on the slopes of the Sierra Madre Mountain Range.