The most common siliceous rock is chert (chert and flint), which is a dense, microcrystalline rock composed of chalcedony and quartz. Chert is the second most abundant chemically precipitated rock after limestone. It occurs in beds and in nodules. Bedded chert consists of siliceous fossils such as diatoms and radiolaria, which form siliceous oozes on the sea floor. As these organisms sink, portions of their shells dissolve near the bottom and reprecipitate in void spaces between shell fragments, resulting in a hard bedded rock. Bedded cherts are common in areas enriched in silica-bearing organisms, as for example near volcanoes where volcanic glass is rapidly altered to produce high-silica concentrations. Similar processes occur in freshwater lakes associated with volcanoes.

Nodular cherts appear to be produced by the alteration of preexisting sedimentary rock. In this process silica distributed throughout the rock dissolves and reprecipitates to form nodules. Mixed sediments, such as siliceous shales and limestones, also appear to be a diagenetic redistribution of siliceous organisms.