Pateros is a low-lying area. It is only about 2.0 meters above sea level with its highest elevation at about 4.0 meters above sea level. Its almost sea level elevation has caused perennial flooding in most of the municipality. High tide in Laguna Bay, which causes backflow of seawater from the Manila Bay into the Pasig River up to Pateros River, coupled with heavy rains, have caused floods in the low-lying areas of Pateros.
The whole municipality is almost of flat terrain with slope rising only up to 2.5% slanting downward towards Laguna Lake. Such terrain and slope makes Pateros very suitable for urban development.
The geology of Pateros is made of quaternary deposits, specifically alluvium (Qal) in the eastern portion and clastic rocks (Qc) in the western area.
Alluvial deposits are characterized by unconsolidated mixture of sand, gravel, and considerable silt and clay derived chiefly from the weathering of pyroclastic and volcanic rocks. They generally occupy the extensive coastal and floodplains around Laguna de Bay. These include recent river deposits covering the older rocks on flat lowlands but exclude the residual soil in extended plains and cultivated uplands.
Clastic rocks are composed principally of tuffaceous sedimentary detritus, which includes waterlaid and reworked sandy tuffs. They are generally bedded and well stratified and are found in places intercolated with thin beds of fine tuff. The major portion of the area west of Laguna Lake, particularly from Pateros to Los Baños, is made up of interbedded tuff, marine sediments and volcanic ash, known as "Laguna Formation" or Guadalupe Tuff. This rock formation is considered very important because of its good water-bearing characteristics.
The rock formation is significant in determining groundwater supply but does not have any bearing on flooding since the major factors affecting flooding are the elevation of the area and of the existing water bodies.