For large-scale sites, difficulties for applying coupled one-dimensional (1D)/2D models for simulating floodplain inundation may be encountered related to data scarcity, complexity for establishing channel–floodplain connections, computational cost, long duration of floods and the need to represent precipitation and evapotranspiration processes. This paper presents a hydrologic simulation system, named SIRIPLAN, developed to accomplish this aim. This system is composed by a 1D hydrodynamic model coupled to a 2D raster-based model, and by two modules to compute the vertical water balance over floodplain and the water exchanges between channel and floodplain. Results are presented for the Upper Paraguay River Basin (UPRB), including the Pantanal, one of the world's largest wetlands. A total of 3965 km of river channels and 140 000 km2 of floodplains are simulated for a period of 11 years. Comparison of observed and calculated hydrographs at 15 gauging stations showed that the model was capable to simulate distinct, complex flow regimes along main channels, including channel-floodplain interactions. The proposed system was also able to reproduce the Pantanal seasonal flood pulse, with estimated inundated areas ranging from 35 000 km2 (dry period) to more than 120 000 km2 (wet period). Floodplain inundation maps obtained with SIRIPLAN were consistent with previous knowledge of Pantanal dynamics, but comparison with inundation extent provided by a previous satellite-based study indicates that permanently flooded areas may have been underestimated. The results obtained are promising, and further work will focus on improving vertical processes representation over floodplains and analysing model sensitivity to floodplain parameters, time step and precipitation estimates uncertainty. Copyright © 2010 John Wiley & Sons, Ltd.