Nodules of chert are rounded to elongated silica-rich lumps that occur within sequences of limestones (commonly chalk and calcilutites). They originate from the diagenesis of an original silica-rich carbonatic ooze, containing remains of organisms like radiolarians or diatoms, which produce shells made of silica. The silica produced by these organisms is amorphous hydrous silica, which is very unstable in oceanic waters and in the sedimentary environment. Consequently, during diagenesis, silica dissolves in the water-rich sediments and starts to migrate through the surrounding carbonates. Where the pH conditions allow it, silica replaces calcium carbonate, producing nodules of microcrystalline quartz that often mimic the orientation of bedding.

Distinguishing features
Nodules of chert in limestone are easily recognizable because of their characteristic shape, hardness (around 7, harder than metal on scratch) and conchoidal fracture. The color of chert nodules is highly variable depending on the trace elements and minerals present. Chert is more resistant to erosion than limestone. Therefore, chert nodules usually stand out compared to the surrounding carbonates.