Cities are considered major contributors to global warming, where carbon emissions are highly embedded in the overall urban metabolism. To examine urban metabolic processes and emission trajectories we developed a carbon flux model based on Network Environ Analysis (NEA). The mutual interactions and control situation within the urban ecosystem of Vienna were examined, and the system-level properties of the city's carbon metabolism were assessed. Regulatory strategies to minimize carbon emissions were identified through the tracking of the possible pathways that affect these emission trajectories. Our findings suggest that indirect flows have a strong bearing on the mutual and control relationships between urban sectors. The metabolism of a city is considered self-mutualistic and sustainable only when the local and distal environments are embraced. Energy production and construction were found to be two factors with a major impact on carbon emissions, and whose regulation is only effective via ad-hoc pathways. In comparison with the original life-cycle tracking, the application of NEA was better at revealing details from a mechanistic aspect, which is crucial for informed sustainable urban management.