Silicified carbonates can appear as silicified carbonate rock layers, or in the form of silicified karsts. The Paleogene Madrid Basin in Central Spain is a foreland basin resulted from the Alpine uplift, an example of silicified carbonates in rock layers. The lithology consists of carbonate and detritus units that were formed in a lacustrine environment. The rock units are silicified where cherts, quartz, and opaline minerals are found in the layers. It is conformable with the underlying evaporitic beds, also dated from similar ages. It is found that there were two stages of silicification within the rock strata. The earlier stage of silicification provided a better condition and site for the precipitation of silica. The source of silica is still uncertain. There are no biogenic silica detected from the carbonates. However, microbial films in carbonates are found, which could suggest the presence of diatoms. 
Karsts are carbonate caves formed from a dissolution of carbonate rocks such as limestones and dolomites. They are usually susceptible to groundwater and are dissolved in these drainage. Silicified karsts and cave deposits are formed when siliceous fluids enter karsts through faults and cracks. The Mid-Proterozoic Mescal Limestone from the Apache Group in central Arizona is classic examples of silicified karsts. A portion of the carbonates are replaced by cherts in early diagenesis and the remaining portion is completely silicified in later stages. The source of silica in carbonates are usually associated with the presence of biogenetic silica; however, the source of silica in Mescal Limestone is from weathering of overlying basalts, which are extrusive igneous rocks that have high silica content.