Local waterlogging often occurs on the steep slopes of clayey–calcareous soils in southwestern France, causing nutrients and pollutants transfer to the river bodies and reduced ecosystems services. These soils developed in the Miocene molassic hill formation and are generally impermeable with abundant traces of hydromorphy and heterogenous spatial distribution. This article aims to describe the hydrological functioning of these soils, based on a cross analysis of pedological, hydrological, and geophysical characterizations. Our experimental site is the catchment area located in Auradé (southwestern France). Here, we analyze the flows at the outlet of the studied watershed together with piezometric and climatic monitoring from September 2020 to September 2021. We show that the hydrological year is divided into three phases: first, a soil recharge phase with an effective rainfall of about 100 mm; second, a saturation phase, when 80% of the effective precipitation is drained mostly by runoff and hypodermic flows; third, a drying phase. Soil waterlogging events usually occur during the saturation phase. They are due to several forms of flow: surface runoff associated with return flow, hypodermic flow caused by the presence of soil layers with lower hydraulic conductivity in the subsurface (swelling clays and plowing sole) and groundwater flow with intermittent connection of the soil water table in the hillside to the alluvial groundwater table. We also conducted independent seismic refraction tomography analyses that validate localized waterlogging patterns along the catchment and open the way to spatializing areas with high waterlogging potential at the scale of the study plot.