The present study focuses on field-scale flow and transport in three-dimensional, heterogeneous, variably saturated formations, for the case in which the flow is coupled to the transport through the dependence of the hydraulic conductivity and water retentivity on solute concentrations. Numerical simulations of flow and transport of both tracer and mixed Na–Ca solutes were employed to analyze long-term effects of the interactions between the soil solution and the soil matrix on water and solute movement, under transient, nonmonotonic flows. The simulated flows were derived from actual irrigation and weather records, along with water uptake by plant roots. Results of this study suggest that enhanced soil solution–soil matrix interactions, induced by soil alkalinity and dilution of the soil solution, may reduce both the mean and the spatial variability of the hydraulic conductivity, and, concurrently, of the velocity. Consequently, enhanced soil solution–soil matrix interactions may slow down the tracer solute movement, decrease the spreading of the tracer solute about its center of mass (particularly in the vertical direction), diminish the skewing of the tracer solute breakthrough, and decrease both the magnitude of the effective retardation factor and the rate at which it approaches its asymptotic value. In addition, our results suggest that under realistic conditions, the three-dimensionality of the flow domain, the periodicity of the rain or irrigation events, along with the substantial redistribution periods between successive events, and the spatial heterogeneity of the hydraulic properties of the variably saturated formation may compensate in part for the adverse effects of soil alkalinity on flow and transport on the field scale. This last finding has practical implications regarding the use of sewage water for irrigation.