Water retention is an important hydrological ecosystem service of active floodplain soils. The aim of the study was to evaluate the soil chemical, physical, and hydrological properties in Fluvisols in three different ecosystems that have an impact on water retention hydrological ecosystem services (WRHESs). We selected 16 localities along the Štiavnica River in Central Slovakia, 8 located in riparian zones (RZ), 5 in arable lands (AL), and 3 in grasslands (GL). Soil samples were collected from two layers (0–10 and 20–30 cm). In the laboratory, the soil physical (soil texture) and soil chemical properties (pH, soil organic carbon content, humic and fulvic acid ratio) were determined. Using undisturbed soil samples, the soil physical characteristics (particle density, bulk density, porosity, and actual soil moisture–SMa) were measured. With the help of pedotransfer functions, hydrological soil properties (field water capacity–FWC, wilting point–WP, available water capacity–AWC) were estimated. The recorded properties differed between the localities, ecosystems, and two layers. The SMa values showed a higher soil water retention potential of extensively used ecosystems, such as GL and RZ. However, the hydrological properties estimated by pedotransfer functions (FWC, WP, AWC) showed a higher soil water retention potential in AL localities. This indicated that for calculations, selected pedotransfer functions (particle size fractions, organic matter, and bulk density) and other soil or ecosystem properties (e.g., vegetation cover, meteorological conditions) have an impact on WRHESs. One such soil factor can be the quality of organic matter. On the basis of the results of the ANOVA, significant differences emerged between the different ecosystems for selected basic chemical, physical, and hydrological properties. The effect of the soil layer on the soil properties was revealed only in the case of SOC. The results indicated the effect of different ecosystems on soil WRHES and the importance of extensively managed ecosystems, such as RZ and GL. From this point of view, the reduction in the RZ and GL areas during a period of the last 70 years is negative. The findings should be taken into account in future sustainable floodplain management and landscape architecture.