Abstract Silicification is the most important process of fossilization resulting in the preservation of internal tissues in plants, thereby providing essential information on the anatomy, life history, and evolution of land plants. However, fundamental knowledge of silica uptake, precipitation, and contribution to in situ plant fossilization is limited. To identify the cellular pathway of aqueous silica and subsequent fluid–wood interaction processes, we investigated upright standing young trees of lodgepole pine (Pinus contorta) in the hot-spring environment of Cistern Spring, Yellowstone National Park, USA. Our multi-method analytical approach using x-ray diffraction, Raman spectroscopy, scanning electron microscopy, and electron probe microanalyses shows that the surficial and internally co-precipitated silica–halite–gypsum assemblage traces the flow of silica-rich fluid and documents fluid retention after short-term hot-spring water immersion and evaporation. Element distribution maps reveal systematic 2D and 3D differences between silica quantities deposited in earlywood and latewood. The distribution of inorganic impurities in cell walls traces the anatomical structure of the wood and indicates rapid migration of homogeneous fluid into the waterlogged organic substrate. Our results show that the preferential pathway of silica-rich fluid into the above-ground wood was through the decorticated periphery which took place during a short-term flooding, ranging from days to weeks, of hot-spring fluid. In conclusion, the fluid retention capability in cellular pore space controls the in situ silicification process. The silicification of trees in growth position is a rapid process in which the in vivo transport of silica-rich fluid upward through the secondary xylem plays an insignificant role.