Several plant species survive in the metal‐contaminated environment by minimization of detrimental effects of metal exposure and cellular accumulation, but little is known about their capability to transform the uptake metal ions into nanoparticles, especially in nonspherical shapes. This work firstly reported the in vivo formation of spherical and rod‐shaped lead nanoparticles (PbNPs) from the uptake lead ions in root cells of water velvet (Azolla pinnata). The energy‐dispersive X‐ray fluorescence analysis revealed the high level of lead (67.21 ± 0.70%) and the modulated levels of sulfur, potassium, and calcium in the treated roots. Fourier‐transform infrared spectroscopy spectral analysis suggested the changes of biochemical constituents in Pb‐treated roots, including carbohydrates, organic compounds, proteins, and nucleic acids. Transmission electron microscope (TEM) images revealed the formation of spherical, short rod, and long rod PbNPs dominantly in epidermal, cortical, and vascular cells in the plant roots, respectively. The analyses of energy‐dispersive X‐ray spectroscopy, high‐resolution TEM, and selected area diffraction TEM indicated the body‐centered tetragonal lattice of lead oxide nanoparticles (PbONPs) in the root cells.