In the Amazon basin, floodplains form a complex mosaic of freshwater systems with differing morphologies, resulting in varied inundation patterns and heterogeneous chemical and ecological characteristics. In this study, we focused on the Janauacá floodplain, a medium‐sized system (786 km2, including the local watershed) located along the Solimões River. Based on in situ and satellite observations acquired from November 2006 to November 2011, we computed water fluxes between the mainstream and the floodplain and examined the temporal dynamics of floodplain storage from river flooding, rainfall, runoff, and exchanges with groundwater through bank seepage for the 5 years from 2006 to 2011. The mainstream was the main input of water to the flooded area, accounting on average for 93% of total water inputs by the end of the water year. Direct precipitation and runoff from uplands contributed less than or equal to 5% and 10%, respectively. The seepage contribution was less than 1%. Model uncertainties, evaluated using Monte Carlo analysis of the input data and model parameters, showed that all water fluxes were relatively well constrained except for outflow through seepage, which had a standard deviation across simulations greater than 60%. The water balance computation was verified using electrical conductivity as an assumed non‐reactive tracer. Except during periods of very low water, the simulated and measured conductivities agreed well. Moreover, conductivity data analysis confirmed that the Janauacá system can be considered homogeneous in terms of electrical conductivity for filling percentages equal to or greater than 40% (i.e., when the water level is above 19.5 m, generally from April to August) but presented large heterogeneities during the rest of the hydrological cycle.

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Flooding dynamics across a medium-size (Janauaca Lake, 786 km 2 ) 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.