A low-cost oyster shell was carried to prepare biogenic calcium carbonate (bio-CaCO₃) to remediate Pb(II) and methyl orange (MO) from contaminated water. The morphology, composition and structure of the material were analyzed mainly by scanning electron microscope (SEM), thermogravimetric analysis (TGA), X-ray fluorescence (XRF). The adsorption of Pb(II) and MO by bio-CaCO₃ was studied by combining batch experiments and microstructure characterization. Batch sorption experiments showed that 45% MO was removed by bio-CaCO₃ (m_sorbent/V_solvent=0.2 g/L, [MO]_initial=60 mg/L). An obviously morphology change took place after MO adsorbed onto bio-CaCO₃. The maximum sorption capacity of bio-CaCO₃ for Pb(II) is 1775 mg/g (pH=5.0, T=298 K), which is higher than that of the traditional nanomaterials such as bentonite and activated carbon. The Pb(II) removal mechanism is expected to be CaCO₃+ Pb(II)→PbCO₃, where the ΔH^θ, ΔS^θ and ΔG^θ of Pb(II) sorption by bio-CaCO₃ (pH=5.0, T=298K) are -7.64 kJ/mol, -17.92 J/(mol·K) and -2.30 kJ/mol, respectively. More regular products with quadrangular structure are formed after Pb(II) adsorption. The results highlight that the bio-CaCO₃ has a high Pb(II) and MO sorption efficiency, demonstrating that it is a promising adsorbent material in environmental pollution management.