Flooding dynamics across a medium‐size (Janauaca Lake, 786 km2) floodplain system along the Amazon/Solimoes River over a 9‐year period (2006–2015) is studied through integration of remote sensing and limited in situ data in hydrologic‐hydrodynamic modelling based on Telemac‐2D model. Model accuracy varies through the hydrological year. We focus on seasonal and interannual spatial variability of water circulation and inundation duration. We highlight strong heterogeneities in water velocity magnitude between the different morphological domains of the floodplain, the highest velocities being encountered in the river‐floodplain channel. In addition to topography, we emphasize the importance of the main channel and the local runoff in controlling the water circulation, at least during part of the hydrological year. From low water to early rising period, local runoff constrains the river incursion across the floodplain, while the rates of main channel rising/receding controls the flood duration. The comparison of several hydrological years highlights the interannual changes of these hydraulic controls and also the influence exerted by prior inundation conditions. While we observed few changes in water velocity distribution among hydrological years, the inundation duration is highly variable. Usually defined by maximum water level, extreme flood events may paradoxically induce positive (up to 40 days) but also negative (up to −20 days) anomalies of inundation duration.