Agricultural soils are characterized by a structure that is strongly dependent on farming practices like tillage and trafficking. These practices can create compacted zones in the soil, thus initiating preferential flow. Two- or three-dimensional models can be used to account for the spatial variability of the soil hydraulic and transport properties. Since it is challenging to obtain such data, it is logical to find simpler approaches. Our objective was to design a one-dimensional (1D) modeling approach that effectively accounts for plot-scale soil structure variability. A 1D dual-permeability model was tested in which compacted soil was represented by a matrix domain and uncompacted soil by a fracture domain and eventually by assuming an additional immobile water region (MIM) in the fracture domain representing compacted clods embedded within the uncompacted soil. Models (1D) were compared with two-dimensional single-porosity (2D_SP) modeling results for water flow and Br− transport based on a previously performed field tracer experiment. Results indicated good agreement between 1D dual-domain approaches (1D_DPERM and 1D_DPERM_MIM) and the 2D_SP representative model simulation results with high model efficiency and with respect to the field observations. This implied that a 1D vertical model description was sufficient to represent plot-scale variability if smaller scale soil structure heterogeneities could be accounted for as effective parameters in dual-domain models. Variation in the mass transfer term had a large effect on the vertical Br− profile distribution. The parameters describing the sizes and shapes of the domains were most relevant for estimating mass transfer between soil structural features in heterogeneous agricultural fields. Still, the calibration of the upscaling approach of two-domain interactions in larger scale models remains challenging.