Floods can mobilize large amounts of unconsolidated material, which also includes large wood in forested river basins. Yet, the influence of the shape and volume of flood hydrographs on wood dynamics in rivers remains poorly understood. Quantitative data on this relation are, however, critically needed to properly address management strategies and to improve the relevant understanding of wood dynamics in rivers. In this work we used a deterministic model, run in a multi-scenario mode, to simulate the transport of wood pieces fully coupled to hydrodynamics. The goal was to analyze how the transport of large wood occurs under different unsteady flood scenarios. We applied the model to two contrasting geomorphic configurations (channelized, single-thread and multi-thread reaches) in the Czarny Dunajec River in Poland, where extensive field observations of wood transport and deposition after floods of different magnitude were available to validate, interpret, and discuss model results. We show that the peak of wood transport is generally reached before the flood peak, and that the wood remobilization ratio is not always positively correlated to peak discharge. We found a positive correlation between the number of mobilized wood pieces and the duration of the rising limb. In addition, hysteresis was observed in the relationship between wood remobilization and discharge. We conclude that numerical modelling allows analysis of wood dynamics in a detail which cannot typically be achieved in field observations. Therefore, modelling improves our understanding of the process and helps disentangling the complex linkages between flood hydrographs and large wood transport dynamics in rivers.