Waste management problems for shallow land burial facilities in the humid eastern United States are usually complicated by slow but continuous movement of wastes through the soil matrix and discrete but rapid pulses of wastes through macropores and fractures. Multiple‐pore‐region models employed to describe flow and solute transport in the soils usually consist of multiple mass transfer coefficients that cannot be measured experimentally, and their effects on subsurface mass transport are poorly understood. The objective of this research was to study the individual and concurrent effects of interaggregate advection and diffusion on mass transport in a structured soil. The interactions of these two mass transfer processes and local solute concentration equilibrium are examined for a heterogeneous soil. Pore region water retention, hydraulic conductivity, and dispersivities, obtained from independent measurements and published calibration results, were used to test a novel three‐pore‐region, one‐dimensional numerical model. Advective and diffusive mass transfer coefficients were estimated using mass transfer equations and fracture spacings published in the literature. The mass transfer coefficients were then varied systematically, and the sensitivity of local fluid pressure and solute concentration nonequilibrium to interregion mass transfer were analyzed. Our results indicated that time‐dependent interaggregate advection and diffusion were important processes controlling solute mobility in heterogeneous media. Under transient flow conditions, interaggregate advection may reduce the significance of interaggregate diffusion that otherwise dominates interaggregate mass transfer under steady state conditions. Nonetheless, the equilibrium of local solute concentrations was 20 times more sensitive to diffusive mass transfer than to advective mass transfer, which suggests that site characterization efforts should be directed more toward the former process. Unfortunately, characterization efforts of this type are not commonplace and if available are frequently ignored because they add a difficult reality to complex waste management problems. Since advective and diffusive mass transfer may be important processes limiting the efficiency of cleanup activities such as pump and treat, it is perhaps time to include the characterization of these processes and quantification of the timescale of physical nonequilibrium in site remediation efforts.