Biogenic cherts
Several organisms produce shells or skeletal fragments that consist of amorphous silica. The most important silica producers are diatoms and radiolarians, unicellular planktonic organisms that live in the upper 200 meters of the water column. Diatoms are single-celled algae (protists) that rely on photosynthesis and produce shells made of opaline silica between 2-200 micrometers (0.002 – 0.2 mm) in diameter. Radiolarians are protozoa that are part of the zooplankton and build 0.1 – 0.2 mm large shells of amorphous silica.

These silica shells slowly settle and accumulate on the seafloor after the death of these organisms: the descent of the shells through the water columns may take up to several weeks or months and, during this time, the remains may be consumed by other organisms or partially dissolve in water. The amorphous silica produced by diatoms and radiolarians is, indeed, very unstable and tends to dissolve in the silica-undersaturated marine waters producing silicic acid (H₄SiO₄). Dissolution processes are stronger in the shallower part of the water column, while deep marine waters, generally more acidic, are less aggressive to silica. The deposition of siliceous ooze on the seafloor is also an indirect effect of the dissolution of carbonates, which increases with depth in present-day oceans. In more acidic, deep waters rich in CO₂ the carbonatic shells of other organisms (like foraminifera) dissolve, enriching the resulting sediment in siliceous ooze. Indeed, in present-day oceans, siliceous oozes accumulate on abyssal plains at more than 4000-5000 meters depth.

Cherts that originate from the lithification of siliceous ooze are classified according to the prevailing microfossils that constitute them as radiolarite (or radiolarian chert), if they are radiolarians, or diatomite, if they are diatoms. In present-day oceans, radiolarian cherts form close to the tropical regions, while diatomites are more common in the arctic and antarctic oceans. There are other organisms that may produce important deposits of siliceous oozes, such as sponges and even cyanobacteria in the Precambrian Earth. Sponges are benthic organisms (living anchored to the seafloor) that produce spicules, which are needle-like skeletal fragments that sustain the organism and offer defense against predators. Spicules can be microscopic to larger than a few millimeters. Cherts consisting of spicules are called spiculite.

After the deposition of siliceous ooze, a series of mineralogical transformations starts to take place. Amorphous, hydrous silica, which is an unstable compound, is substituted first by metastable cristobalite and trydimite, then by microcrystalline or cryptocrystalline quartz. These phase transformations reduce the porosity and cement the original sediment into relatively strong cherts.