AbstractShort‐circuiting flow, commonly experienced in many constructed wetlands, reduces hydraulic retention times in unit wetland cells and decreases the treatment efficiency. A two‐dimensional (2‐D), physically based, distributed modelling approach was used to systematically address the effects of bathymetry and vegetation on short‐circuiting flow, which previously have been neglected or lumped in one‐dimensional wetland flow models. In this study, a 2‐D transient hydrodynamics with advection‐dispersion model was developed using MIKE 21 and calibrated with bromide tracer data collected at the Orlando Easterly Wetland Cell 7. The estimated topographic difference between short‐circuiting flow zone and adjacent area ranged from 0·3 to 0·8 m. A range of the Manning roughness coefficient at the short‐circuiting flow zone was estimated (0·022–0·045 s m−1/3). Sensitivity analysis of topographical and vegetative heterogeneity deduced during model calibration shows that relic ditches or other ditch‐shaped landforms and the associated sparse vegetation along the main flow direction intensify the short‐circuiting pattern, considerably affecting 2‐D solute transport simulation. In terms of hydraulic efficiency, this study indicates that the bathymetry effect on short‐circuiting flow is more important than the vegetation effect. Copyright © 2009 John Wiley & Sons, Ltd.