Porous cups are widely used to extract soil solution for monitoring solute transport; however, it is not always clear how soil heterogeneity influences solute breakthrough sampled by suction cups. The objective of this study was to evaluate the influence of soil heterogeneity on the breakthrough of solute extracted by suction cups. We conducted numerical simulations using the HYDRUS-2D code. Local-scale heterogeneity in hydraulic properties was generated using Miller–Miller scaling theory. Results of the simulations show that effective transport parameters derived from the measured breakthrough curves in the suction cups depended on the location of the suction cup in the heterogeneous flow field. Mean pore water velocities obtained from suction cup measurements ranged by a factor of 1.6 and dispersivities by a factor of 1.5 for the different heterogeneous structures. As a consequence, the arrival time (first moment) of the tracer plume derived from suction cup measurements was accelerated or delayed compared with the homogeneous case. Mass recoveries and suction cup sampling areas were also influenced by the underlying structure. The applied suction in the cup as well as the suction cup sampling area were found to have important effects on the mean pore water velocity, dispersivity, and mass recovery. The effect of variation in applied suction was analyzed using reference point data taken from 10 locations in the undisturbed flow field. Contrary to the general assumption that solute spreading measured with suction cups depends only on the mean pore water velocity, our results show that solute spreading is also influenced by (i) the suction cup sampling area and the deformation of streamlines to the cup, and (ii) the flow channels that are sampled. The numerical simulations indicate that the number of suction cups required for calculating a mean breakthrough curve in the chosen heterogeneous flow field must to be >20.