Surface water flow controls water velocities, water depths, and residence times, and influences sediment and nutrient transport and other ecological processes in shallow aquatic systems. Flow through wetlands is substantially influenced by drag on vegetation stems but is also affected by microtopography. Our goal was to use microtopography data directly in a widely used wetland model while retaining the advantages of the model’s one-dimensional structure. The base simulation with no explicit treatment of microtopography only performed well for a period of high water when vegetation dominated flow resistance. Extended simulations using microtopography can improve the fit to low-water conditions substantially. The best fit simulation had a flow conductance parameter that decreased in value by 70 % during dry season such that mcrotopographic features blocked 40 % of the cross sectional width for flow. Modeled surface water became ponded and flow ceased when 85 % of the cross sectional width became blocked by microtopographic features. We conclude that vegetation drag dominates wetland flow resistance at higher water levels and microtopography dominates at low water levels with the threshold delineated by the top of microtopographic features. Our results support the practicality of predicting flow on floodplains using relatively easily measured physical and biological variables.