In recent years the massive reduction of raw materials production brings a wide scale of problems. Among the most frequent exposes of mining activities belong besides old spoil heaps and sludge lagoons, also the drainage of acidic and highly mineralized mine waters known as “the Acid Mine Drainage” (thereinafter AMD) from old mine workings. The acid mine drainage presents to the surrounding environment a massive problem. These waters are toxic to the plant and animal life, including fishes and aquatic insects. The primary control of the drainage pH and the metal content is the exposure of sulphide minerals to weathering, the availability of atmospheric oxygen, and the sensitivity of non-sulphide minerals to buffer acidity. A geochemical modeling software is increasingly used to solve evolution of the complex chemical systems such as the interaction of acid mine drainage with wall rocks, migration of AMD components. Beyond the better computer facilities it allows to study of thermodynamic properties substances and to enlarge thermodynamic databases. A model is a simplified version of reality based on its observation and experiments. A goal of the modeling process is the tendency to better understand processes taking place inside of the system, the attempt to assume the system’s behaviour in the future or to predict the effect of changed conditions in the system’s environment on the system itself.