We present a physically based Bayesian network model for inference and prediction of flood duration that allows for a deeper understanding of the nexus of antecedent flow regime, atmospheric blocking, and moisture transport/release mechanisms. Distinct scaling factors at the land surface and regional atmospheric levels are unraveled using this Bayesian network model. Land surface scaling explains the variability in flood duration as a function of cumulative exceedance index, a new measure that represents the evolution of the flood in the basin. Dynamic atmospheric scaling explains the cumulative exceedance index using the interaction between atmospheric blocking system and the synergistic model of wind divergence and atmospheric water vapor. Our findings underline that the synergy between a large persistent low-pressure blocking system and a higher rate of divergent wind often triggers a long-duration flood, even in the presence of moderate moisture supply in the atmosphere. This condition, in turn, causes an extremely long-duration flood if the basin-wide cumulative flow prior to the flood event was already high. Thus, this new land-atmospheric interaction framework integrates regional flood duration scaling and dynamic atmospheric scaling to enable the coupling of ‘horizontal’ (for example, streamflow accumulation inside the basin) and ‘vertical’ flow of information (for example, interrelated land and ocean-atmosphere interactions), providing an improved understanding of the critical forcing of regional hydroclimatic systems. This Bayesian model approach is applied to the Missouri River Basin, which has the largest system of reservoirs in the United States. Our predictive model can aid in decision support systems for the protection of national infrastructure against long-duration flood events.