The current benchmark approach for mathematical modelling of floodplain hydrologic regime consists of dynamically coupling one-dimensional (1D) and two-dimensional (2D) models for flow routing along the main channel and the floodplain, respectively. For large-scale sites, floodplain inundation may spread over hundreds of square kilometres and may last for many months and even influence seasonal floods in following years. This paper aims at evaluating the effect of vertical water balance representation on modelling a large-scale floodplain. The Pantanal wetland (140 000 km2; Brazil) is simulated using a 1D/2D coupled model approach, which also considers the representation of vertical water processes over the floodplain. Four scenarios are simulated: Baseline (the reference scenario), NoVertBal (in which the vertical water balance over floodplain is turned off) and ETp+1 and ETp−1 scenarios, characterized by artificially increasing or decreasing daily potential evapotranspiration (ETp) by 1 mm, respectively. The results showed that the effect of the vertical water processes scenarios on channel flow is directly dependent on the lateral exchange of water between the channel and floodplain in the upstream river reach. This influence is stronger when there is a gain of water from the floodplain to the channel. The inclusion of these vertical water processes into floodplain modelling was essential to represent the process of wetting and drying, this effect being more relevant for areas not directly connected to main channels, which is a characteristic of the Pantanal region. Copyright © 2013 John Wiley & Sons, Ltd.