The lateral dimension of fluvial hydrosystems encompasses the interactions between main and floodplain channels, creating diverse environmental conditions that shape ecosystem metabolism in space and time. Most studies on the metabolism of fluvial hydrosystems (i.e., defined by the balance between Gross Primary Production (GPP) and Respiration (ER)) have focused on main channels, overlooking the lateral floodplain dimension. We developed a novel approach to quantify temporal dynamics of lateral channel connectivity and we further assess their influence on ecosystem metabolism. To this end, we used hourly water table and temperature data over one year in nine floodplain channels and two main channels of the French Upper Rhône to compute a Synchronism Index (SI) describing the degree of hydrological coupling between floodplain and main channels. In addition, concurrent continuous dissolved oxygen measurements enabled metabolism quantification of each floodplain channel. Our results show (i) the relevance of SI in characterizing lateral connectivity dynamics, and (ii) a consistent increase in GPP and ER in desynchronized channels. This suggests that reduced hydraulic constraints favor higher primary production and organic matter accumulation, leading to enhanced respiration. This study seems pioneering in revealing how variability in lateral connectivity shapes metabolism in fluvial hydrosystems and provides initial knowledge for management in a context of intensified disconnection of floodplain ecosystems.