Any buffer system has a certain potential reserve, which controls equilibrium and keeps one of the equilibrium parameters constant. The lack of information about the metal buffer properties of ecosystems can be explained by the absence of the quantitative theory that may predict their buffer behaviour. The low buffer capacity of ecosystems, that are unable to preserve a constant equilibrium parameter, leads to disastrous environmental consequences. We have proved that buffering of intensive thermodynamic variables in ecosystems significantly differ from the classical buffering in aqueous solutions. Whereas buffering in a mono-phase system is controlled by homogeneous equilibria, heterogeneous equilibria between solid (mineral) and aqueous phases, control such thermodynamic parameters of ecosystems, as the concentration, temperature and pressure. An essential characteristic of any buffer is its buffering capacity “β”, which defines the change of equilibrium concentration of mobile components, as a result of their addition to or removal from the system. In this paper, a novel ion-molecular buffer approach for estimating buffer capacities for natural water – mineral equilibria has been developed. Using this approach, the buffer capacity regard with any component of the heterogeneous system can be assessed. A remarkable proportional relation between different capacities with respect to ions of the compound distributed between two phases has been established. The influence of major thermodynamic parameters, as temperature, pH and main chemical component concentrations of natural waters upon system buffer capacities has been investigated. It is expected that such approach will help to predict long-term effects in natural pollutant diminishing as a remediation option. The obtained results are indented to provide researchers with a compulsory tool to set reliable limits of ion (including metal) levels in ecosystems.