In this study, the electrodeposition technique has been used to deposit low concentrations of highly toxic lead (Pb) cations into a solution of nitrate at a constant potential of − 1 V on fluorine-doped tin oxide electrodes (FTO). Monitoring of the reaction was conducted with the assistance of a computerized potentiostat/galvanostat setup, in cyclic voltammetry and in situ chronoamperometry modemodes. X-ray diffraction, scanning electron microscopy, energy-dispersive X-Ray, and ultraviolet–visible spectroscopy techniques were used to examine the crystal structure, morphology, and optical properties of the lead deposits, respectively. Pb regular micro-hexagons have been identified; their size and density were significantly influenced by the cationic precursor’s concentration. The correlation between the morphological and crystallographical structures of the electrodeposits was discussed. Based on chronoamperometric measurements, a mechanism for the growth of Pb deposits on FTO substrate has been proposed. Based on the reported results, electrodeposition processes of low heavy metals concentrations in contaminated water could be optimized using the eco-friendly electrodeposition technique.