This work is the fifth 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 used to develop models that describe species transport and single-fluid-phase flow through a porous medium system in varying physical regimes. Classical irreversible thermodynamics formulations for species in fluids, solids, and interfaces are developed. Two different approaches are presented, one that makes use of a momentum equation for each entity along with constitutive relations for species diffusion and dispersion, and a second approach that makes use of a momentum equation for each species in an entity. The alternative models are developed by relying upon different approaches to constrain an entropy inequality using mass, momentum, and energy conservation equations. The resultant constrained entropy inequality is simplified and used to guide the development of closed models. Specific instances of dilute and non-dilute systems are examined and compared to alternative formulation approaches.