Mobilization of large wood in river channels during floods represents a hazardous factor, augmenting flood risk and endangering infrastructures such as bridges, weirs, and reservoir dams. A hybrid modeling approach combining numerical models with field-based surveys has been recently used to elucidate the processes of LW entrainment and deposition in rivers. We used two-dimensional hydraulic modeling performed in HEC-RAS to simulate LW entrainment in two valley bottom segments of the Dyje River, Czechia, where LW deposition is a significant hazard to the dam of the downstream Znojmo reservoir. We surveyed all LW pieces in the inundation area of the 2002 extreme (>Q100) flood and simulated their entrainment for eight flood scenarios (1–100-year recurrence interval). We used the equations of Braudrick and Grant (2000, https://doi.org/10.1029/1999WR900290) to calculate the LW entrainment threshold; we introduced coefficient k accounting for the incomplete submersion of LW pieces resting on an inclined surface into the original equations. Four entrainment categories — stable, wetted stable, wetted buoyant, and wetted entrained — were defined, and the proportion of LW pieces in each category was calculated for the flood scenarios. We found marked differences in entrainment categories for respective flood scenarios between the two valley segments. These were attributed to the differences in pieces' dimensions, their spatial distribution within the inundation area, and valley-bottom topography, which affects the hydraulic conditions for a given discharge. The presented approach enables the calculation of the LW quantity potentially mobilized by the flood of a certain magnitude indicating the degree of potential risk for the infrastructures located downstream.