The erosion, transport and deposition of sediments in small valley reservoirs represent a significant impact on their operations, mainly with regard to reducing the volume of their accumulation. The aim of this study is a comparison and uncertainty analysis of two modelling concepts for assessment of soil loss and sediment transport in a small agricultural catchment, with an emphasis on estimating the off-site effects of soil erosion resulted in sedimentation of a small water reservoir. The small water reservoir (polder) of Svacenicky Creek which was built in 2012, is a part of the flood protection measures in Turá Lúka and is located in the western part of Slovakia, close to the town of Myjava. The town of Myjava in recent years has been threatened by frequent floods, which have caused heavy material losses and significantly limited the quality of life of the local residents. To estimate the amount of soil loss and sediments transported from the basin, we applied two modelling concepts based on the USLE/SDR and WaTEM/SEDEM erosion models and validated the results with the actual bathymetry of the polder. The measurements were provided by a modern Autonomous Underwater Vehicle (AUV) hydrographic instrument. From the sediment data measured and the original geodetic survey of the terrain conducted at the time of the construction of the polder, we calculated changes in the storage volume of the polder during its four years of operation. The results show that in the given area, there has been a gradual clogging of the bottom of the polder caused by water erosion. We estimate that within the four years of the acceptance run, 10,494 m3 of bottom sediments on the Svacenicky Creek polder have accumulated. It therefore follows that repeated surveying of the sedimentation is very important for the management of the water reservoir.