Material excavated from a trench dug to expose the Rhynie Cherts Unit of the Dryden Flags Formation included blocks of Rhynie chert up to 50 cm thick and comprising the full thickness of plant-bearing chert beds. These blocks, and others collected as float, display a variety of macro-textures typical of silicification at the terrestrial surface and in shallow water. On sandy terrestrial surfaces, autochthonous and allochthonous plant debris and plant rhizomes are well preserved, but aerial axes generally decayed prior to silicification. In shallow water, clonal plants, particularly Rhynia, are preserved with aerial axes in growth position, supported by microbial mats and meshworks. Preservation of such delicate fabrics required the creation of a load-bearing framework early in the silicification process, to prevent crushing during early burial.

On the microscale, plant taphonomy reveals characteristic features due to plant decay prior to silicification in both wet and dry conditions, and also during the silicification process. Silicification of plants was frequently very rapid, preserving delicate transient features such as spore germination and ejection of sperm cells from antheridia. In situations where plant tissue continued to decay during silicification, the process was slower.