In this paper, we macroscopically describe the traffic dynamics in heterogeneous transportation urban networks by utilizing the Macroscopic Fundamental Diagram (MFD), a widely observed relation between network-wide space-mean flow and density of vehicles. A generic mathematical model for multi-reservoir networks with well-defined MFDs for each reservoir is presented first. Then, two modeling variations lead to two alternative optimal control methodologies for the design of perimeter and boundary flow control strategies that aim at distributing the accumulation in each reservoir as homogeneously as possible, and maintaining the rate of vehicles that are allowed to enter each reservoir around a desired point, while the system's throughput is maximized. Based on the two control methodologies, perimeter and boundary control actions may be computed in real-time through a linear multivariable feedback regulator or a linear multivariable integral feedback regulator. Perimeter control occurs at the periphery of the network while boundary control occurs at the inter-transfers between neighborhood reservoirs. To this end, the heterogeneous network of San Francisco is partitioned into three homogeneous reservoirs and the proposed feedback regulators are compared with a pre-timed signal plan and a single-reservoir perimeter control strategy. Finally, the impact of the perimeter and boundary control actions is demonstrated via simulation by the use of the corresponding MFDs and other performance measures. A key advantage of the proposed approach is that it does not require high computational effort and future demand data if the current state of each reservoir can be observed with loop detector data. (C) 2013 Elsevier Ltd. All rights reserved.