The Czech landscape has undergone various changes over the last 100 years and has been mainly adapted agriculturally for economic purposes. This has resulted, among other things, in reservoirs being clogged with sediment. The Vrchlice Reservoir was built in 1970 to supply drinking water for around 50,000 inhabitants, and increased sedimentation has been detected in the reservoir in recent years. Water erosion and sediment transport were modeled with WaTEM/SEDEM. Sediment volumes were measured in eight ponds across the watershed for calibration purposes. Modeled results from ponds in watersheds covered mostly with arable lands generally corresponded with the measured values. Although in forested watersheds, the measured sediment volumes greatly exceeded modeled sediment yields, indicating high uncertainty in using USLE-based models in non-agricultural watersheds. The modeled scenarios represented pre-Communist, Communist, and post-Communist eras. For these periods WaTEM/SEDEM was used to evaluate three isolated effects: the effects of various crops on arable lands, the effects of farmland fragmentation, and finally the effects of changes in land use. The change in crops proved to be an important factor causing high siltation rate (potential 23% reduction in sediment yield for historical periods), and land fragmentation played the second important role (potential 15% reduction in sediment yield can be reached by land fragmentation). Across all scenarios, the lowest sediment yield and reservoirs siltation rates were obtained from the pre-Communist and Communist crop share under current land use conditions, and current land use with farmland fragmentation implemented, as it was re-constructed for the pre-Communist era. This supports the idea that the introduction of green areas within arable lands are beneficial to the landscape and can help reduce soil erosion and reservoir siltation.