Given the increasing consciousness toward the environmental footprint of mobility, accommodating environmental objectives in existing transport planning strategies is imperative for research and practice. In this paper, we use the link macroscopic fundamental diagram (MFD) model to develop optimal routing strategies that minimize total system emissions (TSE) in multiple origin-destination (OD) networks. Piecewise linear (PWL) functions are used to approximate MFD for individual links, and to define link-level emissions. Dynamic network constraints, non-vehicle holding constraints, and convex formulations of the PWL functions are considered. Thus, the system-optimum dynamic traffic assignment (SO-DTA) problem with environmental objectives is formulated as a mixed integer linear program (MILP). Finally, on a synthetic network, numerical examples demonstrate the performance of the proposed framework.