This paper demonstrates the power of material flow analysis (MFA) for designing waste management (WM) systems and for supporting decisions with regards to given environmental and resource goals. Based on a comprehensive case study of a nationwide WM-system, advantages and drawbacks of a mass balance approach are discussed. Using the software STAN, a material flow system comprising all relevant inputs, stocks and outputs of wastes, products, residues, and emissions is established and quantified. Material balances on the level of goods and selected substances (C, Cd, Cr, Cu, Fe, Hg, N, Ni, P, Pb, Zn) are developed to characterize this WM-system. The MFA results serve well as a base for further assessments. Based on given goals, stakeholders engaged in this study selected the following seven criteria for evaluating their WM-system: (i) waste input into the system, (ii) export of waste (iii) gaseous emissions from waste treatment plants, (iv) long-term gaseous and liquid emissions from landfills, (v) waste being recycled, (vi) waste for energy recovery, (vii) total waste landfilled. By scenario analysis, strengths and weaknesses of different measures were identified. The results reveal the benefits of a mass balance approach due to redundancy, data consistency, and transparency for optimization, design, and decision making in WM.