Manganese (Mn) dendrites are a common type of mineral dendrite that typically forms two-dimensional structures on rock surfaces. Three-dimensional (3-D) Mn dendrites in rocks have rarely been reported, and so their growth implications have largely escaped attention. Here, we combined high-resolution X-ray and electron-based data with numerical modeling to give the first detailed description of natural 3-D Mn dendrites (in clinoptilolite tuffs) and elucidate their growth dynamics. Our data show that 3-D dendrite growth occurred by accretion of Mn-oxide nanoparticles formed when Mn-bearing fluids mixed with oxygenated pore water. The geometry of the resulting structures is sensitive to ion concentrations, the volume of infiltrating fluid, and the number of fluid pulses; thus, 3-D dendrites record the hydrogeochemical rock history.