For the Czech Republic to recover from the effects of past mismanagement, it is necessary to determine how its landscape management can be improved holistically by reinforcing the small water cycle. We conducted a scenario analysis across four time periods using SWAT (Soil and Water Assessment Tool) to determine the effects of land use, land management, and crop rotation shifts since the 1800s in what is now the Czech Republic. The 1852 and 1954 land-use scenarios behaved the most similarly hydrologically across all four scenarios, likely due to minimal landscape transformation and the fact that these two scenarios occur prior to the widespread incorporation of subsurface tile drainages across the landscape. Additionally, the crop rotation of 1920–1938 reinforces the small water cycle the most, while that of 1950–1989 reinforces the small water cycle the least. Diversified crop rotations should be incentivized to farmers, and increasing the areas of forest, brush, and permanent grassland should be prioritized to further reinforce the small water cycle. It is necessary to foster relationships and open communication between watershed managers, landowners, and scientists to improve the small water cycle and to pave the way for successful future hydrological modeling in the Czech Republic.