In order to investigate the adsorption characteristics of Cu²⁺, Zn²⁺, and Mn²⁺ on natural diatomite in liquid/solid systems and to provide reliable theoretical support for the application of these materials, we conducted a series of adsorption studies. The results revealed a non-monotonic relationship between the adsorption capacity of natural diatomite and ion concentration. The maximum adsorption capacities for Cu²⁺, Zn²⁺, and Mn²⁺ were found to be 3.56, 6.23, and 3.82 mg·g⁻¹, at concentrations of 200, 500, and 300 mg·L⁻¹. Optimal adsorption conditions were determined by investigating environmental factors such as pH and temperature: pH 6, temperature 30 °C, and contact time 40 min. The adsorption kinetics were found to be in accordance with the pseudo-second-order model (R² > 0.997). Fitting adsorption isotherms for Cu²⁺, Zn²⁺, and Mn²⁺ using various models revealed that the Langmuir (R² > 0.993), Temkin (R² > 0.953), and Freundlich (R² > 0.997) models most accurately describe their adsorption behaviour. Thermodynamic analysis confirmed that adsorption is a spontaneous, endothermic, physical process (ΔG° < 0, ΔH° > 0, ΔS° > 0) and that the overall adsorption rate is limited by micropore adsorption. Consequently, natural diatomaceous earth can serve as an efficient, low-cost adsorbent for removing heavy metals from contaminated water.