A major target of strategies toward a more sustainable resource use must be to find ways of remaining within the planetary boundaries, not only by reducing overall resource use but also through keeping within the system what we are already using. This makes it necessary to take a systemic perspective and look at the whole life cycle of joint product systems, raw material inputs, and respective emissions. Knowing and understanding the dynamics of material stocks and flows may be a first step toward managing them. In the context of society, this approach is known as socioeconomic metabolism and is increasingly applied especially in regional and urban contexts. Here, we introduce material flow analysis as a possible method for constructing and evaluating material and energy flows to gain an insight into the flows of specific substances within the anthropogenic system. We show the main characteristics and applications as well as possible limitations of such a modeling approach and conclude with implications for a further development of such methods to enable a shift from analysis to assessment and strategy building that reflects sustainability principles and goes beyond efficiency.