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This paper outlines the application of a special Environmental Management Information System (EMIS) as combination of discrete event simulation with ecological material flow analysis for a selected production process. The software tool serves as decision aid for economic as well as ecological business problems. A combined view of the material flow as well as job-oriented view on an enterprise allows for a unified and efficient model building process. This contribution summarizes the underlying concepts and the experiences with the development and utilization of a suitable software tool following this integrated view and describes the concrete problems and solutions at the example of modeling a complex semiconductor fabrication.