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Check dams act as soil collectors during floods, thus retaining a large amount of sediments. The estimation of the soil volumes stored behind a check dam is a key activity for a proper design of these control works and for evaluation of soil delivery after restoration measures at watershed level. Several topographic techniques have been proposed for this activity, but the sediment wedge mapping tools are complex and time consuming. Conversely, the use of unmanned aerial vehicles (UAVs) has been proposed to support aerophotogrammetric techniques for several survey activities with promising results. However, surveys by UAVs have never applied to calculate the size of the sediment wedge behind check dams that are built in fire-affected watersheds, where soil loss and sediment transport may be high after a wildfire. To fill this gap, this study evaluates the efficiency and efficacy of aerophotogrammetric surveys using UAVs to estimate the volume of the sediments stored behind ten check dams, built as post-fire channel treatment in a forest watershed of Castilla La Mancha (Central Eastern Spain). The results of the aerophotogrammetric technique were compared to traditional topographic surveys using a total station and GNSS/RTK, assumed as reference. The estimation of sediment wedge volume provided by UAVs was more accurate (mean RMSE of 0.432), extensive (density of mapped points of 328 m−2) and quick (two days of fieldwork) compared to surveys using the topographic method (RMSE < 0.04 m, six days of field work and density of mapped points of 0.194 m−2) by the topographic method. The differences in the sediment volume estimated by the two methods were not significant, but the UAV method was more accurate for the larger check dams. Moreover, a significant correlation was observed between the volume estimates provided by the two methods, shown by a coefficient of determination close to 0.98. Overall, these results propose a larger use of the aerial surveys for mapping activities in channels regulated by check dams, such as those built for restoration of fire-affected forest watersheds.