Large wood tends to be deposited in specific geomorphic units within rivers. Nevertheless, predicting the spatial distribution of wood deposits once wood enters a river is still difficult because of the inherent complexity of its dynamics. In addition, the lack of long-term observations or monitored sites has usually resulted in a rather incomplete understanding of the main factors controlling wood deposition under natural conditions. In this study, the deposition of large wood was investigated in the Czarny Dunajec River, Polish Carpathians, by linking numerical modelling and field observations so as to identify the main factors influencing wood retention in rivers. Results show that wood retention capacity is higher in unmanaged multi-thread channels than in channelized, single-thread reaches. We also identify preferential sites for wood deposition based on the probability of deposition under different flood scenarios, and observe different deposition patterns depending on the geomorphic configuration of the study reach. In addition, results indicate that wood is not always deposited in the geomorphic units with the highest roughness, except for low-magnitude floods. We conclude that wood deposition is controlled by flood magnitude and the elevation of flooded surfaces in relation to the low-flow water surface. In that sense, the elevation at which wood is deposited in rivers will differ between floods of different magnitude. Therefore, together with the morphology, flood magnitude represents the most significant control on wood deposition in mountain rivers wider than the height of riparian trees.