The main objectives of waste management are environmental preservation, the safeguarding of human health, and natural resources conservation. Material flow analysis/ substances flow analysis (MFA/SFA) method takes into account the consideration of the “metabolic” system of waste management, which means monitoring waste flows and substances within the model for waste management, and examining all inputs and outputs in the system, as well as their evaluation and comparison. Modeled scenarios in the Banjaluka region of the Republic of Srpska (RS) were developed in accordance with both the European Union (EU) and RS legislation, as well as relevant municipal waste management strategic documents. Modeled municipal solid waste (MSW) management scenarios are compared with the current waste management system. Using MFA/SFA (waste flow, carbon, and nitrogen), a complete view of flow, transformations, and final waste disposal and substances in modeled scenarios of waste management is realized. Results of this study suggest that in the future, more activity should be based on the separate collection and recycling, compared to the current, inadequate MSW management system that is based only on the disposal of waste. The combination of material and substance flows analyses is an effective tool in the decision-making process for the development and improvement of MSW management.