Meteorological simulations using hydrological models are now important for water and environmental resource management. The hydrological system of a catchment cannot be measured precisely in practice. A combination of limited measurements available in space, as well as a need to extrapolate information from available measurements in time, led to the use of the hydrological model. The aim of the study was to assess the catchment retention capacity of the flysh catchments of the Smugawka (19°47-49°33) and Mszanka (20°15-49°44′) rivers located in the Beskid Wyspowy, southern Poland. Due to the large heterogeneity of the catchment area and the limitations of the measurement technique, SWAT+ was employed in our study. Forested and pasture areas had higher soil water retention potential, while lower soil retention potential values are correlated with agricultural areas. Surface runoff of both catchments correlated negatively with soil water retention potential, evapotranspiration, and positively with mean annual precipitation. Soil moisture was related to electrical conductivity and inversely correlated with mean annual precipitation. A study has shown that SWAT+ can be applied to calculate the mean annual continuous evapotranspiration for meadows, forests, and agricultural areas. Curve number may be used as a tool for water retention in floodplains. In line with the physical-based SWAT+, the Landscape Hydric Potential (LHP) index can be incorporated into the existing meteorological data models. In the future, watershed models based on water balance should be developed to increase resilience in the flysh Carpathian mountains to climate change.