In this study, we report the feasibility of using nano chamomile waste (NCW) as a selective solid phase extractor for heavy metal ions. The experimental parameters including pH (1.0–6.0), metal ion concentration (10–100 mole), adsorbent dose (10–1000 mg), and biosorption time (0.5–90 min) were altered by using the batch technique to optimize the maximum capacity of this new biosorbent. The experimental data by NCW agreed with both Freundlich and Langmuir models (R2 =0.999) with maximum uptake capacities of 621.6 mgg–1 (3 mmolg–1) for Pb (II), 163.9 mgg–1 (2.58 mmolg–1) for Cu (II), and 522.7 mgg–1 (9.36 mmolg–1) for Fe (III). In addition, the values of metal uptake as a function of time agreed with the kinetic pseudo-second-order model. The kinetic experiments confirmed the fast accessibility of metal ions to the biosorbent surface resulting in equilibrium within 30 s. NCW was also characterized using FT-IR spectra and the crystallinity of the biosorbent was characterized using X-ray diffraction (XRD). The morphological characterization and particle size of NCW were obtained using SEM and TEM, respectively. Our method was investigated to measure Pb (II), Cu (II), and Fe (III) with a certain spiked amounts in natural water samples such as groundwater (GW), drinking tap water (DTW), natural drinking water (NDW), Nile River water (NRW), seawater (SW), and wastewater (WW). A removal efficiency of ≥98% was obtained for all collected samples using batch experiments and without matrix interferences. Considering its cheap source, simple, economic and fast uptake process, NCW can be used as a low-cost nano biosorbent for the removal of metal ions from natural water samples.