For the activities of the mining industry land, equipment, material, and energy are used. During operation material and energy flows such as overburden, dead rock, tailings, wastewater, exhaust air, dust, energy, abrasion, coolant and lubricant losses, are released. These released material and energy flows are nearly always without value for the raw material supply chain as they are not production targets. Instead, they have negative effects on the economy and ecology and are, therefore, referred to as non-intended. The knowledge of the quantities and qualities of these non-intended outputs as a function of the processes and their parameters is the basis for technical and economical measures. A methodology for the acquisition and assessment of the material and energy flows in the mining industry was developed and tested at the Technical University Berlin, Germany. For that purpose and based on a system analysis in different mines, all relevant material and energy flows were assigned to individual processes. Causal relationships, possible interactions, quantities, and qualities were examined as functions of system parameters. Finally, a technical and economic evaluation was performed.