The last decade has witnessed increasing interest in the study of urban stocks and flows. This paper provides a literature review for different studies of urban stocks and flows. The review shows that urban stocks and flows studies can be categorized according to their output and spatial resolution: The first type of studies uses a lower scale of spatial resolution and focuses on the city as one unit. The second type of studies uses a higher spatial resolution to analyze stocks and flows of sub-areas of the city and is therefore able to produce maps to visualize their results. Both types of studies can either use recent data in a non-dynamic way, or use a time series of data, which allows for the investigation of the city’s development over time. Information about input and output data per study was determined. The literature review also identifies problems associated with current studies, which are related to data availability and accuracy, assumptions, simplifications, and errors. The paper proposes that stocks and flows studies could benefit greatly from the linkage with a standardized semantic 3D city model, such as defined by the CityGML standard. Feedback on CityGML and its ADE capabilities to model urban metabolism is provided.