As a first step toward understanding the role of sedimentary structures in flow and transport through porous media, this work deterministically examines how small‐scale laboratory‐measured values of hydraulic conductivity relate to in situ values of simple, artificial structures in an intermediate‐scale (10 m long), two‐dimensional, heterogeneous, laboratory experiment. Results were judged based on how well simulations using measured values of hydraulic conductivities matched measured hydraulic heads, net flow, and transport through the tank. Discrepancies were investigated using sensitivity analysis and nonlinear regression estimates of the in situ hydraulic conductivity that produce the best fit to measured hydraulic heads and net flow. Permeameter and column experiments produced laboratory measurements of hydraulic conductivity for each of the sands used in the intermediate‐scale experiments. Despite explicit numerical representation of the heterogeneity the laboratory‐measured values underestimated net flow by 12–14% and were distinctly smaller than the regression‐estimated values. The significance of differences in measured hydraulic conductivity values was investigated by comparing variability of transport predictions using the different measurement methods to that produced by different realizations of the heterogeneous distribution. Results indicate that the variations in measured hydraulic conductivity were more important to transport than variations between realizations of the heterogeneous distribution of hydraulic conductivity.