The geology of Guam formed as a result of mafic, felsic and intermediate composition volcanic rocks erupting below the ocean, building up the base of the island in the Eocene, between 33.9 and 56 million years ago. The island emerged above the water in the Eocene, although the volcanic crater collapsed. A second volcanic crater formed on the south of the island in the Oligocene and Miocene. In the shallow water, numerous limestone formations took shape, with thick alternating layers of volcanic material. The second crater collapsed and Guam went through a period in which it was almost entirely submerged, resembling a swampy atoll, until structural deformation slowly uplifted different parts of the island to their present topography. The process of uplift led to widespread erosion and clay formation, as well as the deposition of different types of limestone, reflecting different water depths.

Guam began to form in the late middle Eocene with the development of the Facpi Formation.^[1] The Facpi Formation was associated with submarine volcanism, evidenced by pillow basalt in flow rocks from that series. The Facpi Formation forms the basement volcanic rock of Guam and was deposited when the island was formed in close proximity to the Palau-Kyushu Ridge.

The second major volcanic episode is associated with the Alutom Formation which was formed in the late Eocene. The formation contains basalt and andesite, as well as volcanic breccia with component dacite pebbles and cobbles and tuff shale cemented together with calcite. The presence of the dacite pebbles and correlation with dacitic lava flows on Saipan, dacite flows likely preceded andesite eruptions on Guam. Although the Alutom Formation does not contain many carbonates besides the calcite, the presence of limestone fragments in upper units suggests that limestone formations existed close by. Stabile shallow water reef-forming environments by the end of the Eocene gave way to violent volcanic eruptions in the Oligocene. The island's central caldera collapsed as a result of uplift and faulting.^[2]

In the Oligocene, the Tenjo structural block formed as Eocene volcano eroded.

Groundwater supplies about 80% of the island's freshwater needs, with greater reliance on surface water in the south. Streams are only found in southern Guam, where volcanic rock with low-permeability slows the infiltration of rainwater into the ground. In the north, a limestone karst landscape quickly absorbs water. On Guam, freshwater forms a lens, with a transitional zone of brackish water to salt water underneath it.

Throughout the island, the freshwater lens is nearly flat, with water levels less than eight feet. In some cases, the lens extends into fractures in the volcanic rock, but for the most part, it is contained in limestone in the north. Minor areas of perched water occur in limestone, atop nearly impermeable volcanic rocks at different points.

The island has some ability to extract groundwater for drinking water and other uses, but there is a constant risk of saltwater intrusion. Well measurements indicate that further inland, thicker rocks moderate the effect of tide cycles in wells, such that wells within one mile of the coast had a range of half a foot, which dropped to 0.05 feet further inland. The Guam Waterworks Authority, Guam Environmental Protection Agency, the Air Force and the Navy manage the 180 wells throughout the island. A combination of high-permeability rock, over pumping and overcrowding of wells resulted in 32% of wells (measured in data from the early 1960s through 1997) exceeding a guideline of 250 mg/L chloride concentration.^[6]