Purpose of this study is to evaluate the capacity of a previously-developed upscaling approach to adequately describe main solute transport processes including the capture of late-time tails under changing boundary conditions. Potential factors that impact the performance of upscaling methods, including temporal variations in mass transfer rates and mass distributions were investigated. Advective-dispersive contaminant transport in a 3D heterogeneous domain was simulated and used as a reference solution. Equivalent transport under homogeneous flow conditions were then evaluated applying the Multi-Rate Mass Transfer (MRMT) model. The random walk particle tracking method was used to solve the solute transport for heterogeneous and homogeneous-MRMT scenarios under steady state and transient conditions.