This work is the fourth in a series of papers on the thermodynamically constrained averaging theory (TCAT) approach for modeling flow and transport phenomena in multiscale porous medium systems. The general TCAT framework and the mathematical foundation presented in previous works are built upon by formulating macroscale models for conservation of mass, momentum, and energy, and the balance of entropy for a species in a phase volume, interface, and common curve. In addition, classical irreversible thermodynamic relations for species in entities are averaged from the microscale to the macroscale. Finally, we comment on alternative approaches that can be used to connect species and entity conservation equations to a constrained system entropy inequality, which is a key component of the TCAT approach. The formulations detailed in this work can be built upon to develop models for species transport and reactions in a variety of multiphase systems.