This chapter presents an environmentally integrated manufacturing system analysis for companies looking for the benefits of environmental management in achieving high productivity levels. When the relationship between environmental costs and manufacturing decisions is examined, it can be seen that the productivity of the company can be increased by using an environmentally integrated manufacturing system analysis methodology. Therefore, such a methodology is presented and the roadmap for generating environmentally friendly and economically favorable alternative waste management solutions is elaborated. The methodology combines data collection, operational analysis of the manufacturing processes, identification of wastes, and evaluation of waste reduction alternatives. The presented methodology is examined in a car battery manufacturing plant, which generates hazardous wastes composed of lead. It is aimed to decrease the wastes derived from the production so that the efficiency in raw materials usage is increased and the need for recycling the hazardous wastes is decreased.