The main goal in this paper is to show how to use the developed buffer theory for assessing and predicting the long-term phenomena of attenuation and natural remediation of ionic pollutants in contaminated aquatic ecosystems, as well as for analyzing the way by which metals move and transform within the environment, the distribution of metals in ecosystems, their deposition and cycling in the terrestrial environment. The buffer theory is based on the rigorous thermodynamic analysis of complex chemical equilibria under environmental conditions in aquatic ecosystems, as the natural waters and soils. It has been established that both homogeneous and heterogeneous systems manifest a buffer action towards all their soluble components. The buffer properties in relation to the solid phase components are amplified with an increase of solubility due to protolytic or complex formation equilibria in saturated solutions. It has been established that the buffer capacities of components are mutually proportional, whereas for heterogeneous systems these relationships depend on the stoichiometric composition of solid phases. The use of the developed buffer approach may yield extended knowledge and a deeper understanding of the processes that control the concentrations of components. A number of the important conclusions concerning the investigated buffer systems have been made. The obtained results are indented to provide researchers with a tool needed to help them to set reliable limits of ion (metal) levels in the environment.