Congestion pricing schemes have been traditionally derived based on analytical representations of travel demand and traffic flows, such as in bottleneck models. A major limitation of these models, especially when applied to urban networks, is the inconsistency with traffic dynamics and related phenomena such as hysteresis and the capacity drop. In this study we propose a new method to derive time-varying tolling schemes using the concept of the Network Fundamental Diagram (NFD). The adopted method is based on marginal cost pricing, while it also enables to account realistically for the dynamics of large and heterogeneous traffic networks. We derive two alternative cordon tolls using network-aggregated traffic flow conditions: a step toll that neglects the spatial distribution of traffic by simply associating the marginal costs of any decrease in production within the NFD to the surplus of traffic; and a step toll that explicitly accounts for how network performance is also influenced by the spatial variance in a 3D-NFD. This pricing framework is implemented in the agent-based simulation model MATSim and applied to a case study of the city of Zurich. The tolling schemes are compared with a uniform toll, and they highlight how the inhomogeneous distribution of traffic may compromise the effectiveness of cordon tolls.