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.