Thickness and stratigraphic settings of soils covering slopes potentially control susceptibility to initiation of rainfall-induced shallow landslides due to their local effect on slope hydrological response. Notwithstanding the relevance of the assessment of hazard to shallow landsliding at a distributed scale by approaches based on a coupled modelling of slope hydrological response and slope stability, the spatial variability of soil thickness and stratigraphic settings are factors poorly considered in the literature. Under these premises, this paper advances the well-known case study of rainfall-induced shallow landslides involving ash-fall pyroclastic soils covering the peri-Vesuvian mountains (Campania, southern Italy). In such a unique geomorphological setting, the soil covering is formed by alternating loose ash-fall pyroclastic deposits and paleosols, with high contrasts in hydraulic conductivity and total thickness decreasing as the slope angle increases, thus leading to the establishment of lateral flow and an increase of pore water pressure in localised sectors of the slope where soil horizon thickness is less. In particular, we investigate the effects, on hillslope hydrological regime and slope stability, of irregular bedrock topography, spatial variability of soil thickness and vertical hydraulic heterogeneity of soil horizons, by using a coupled three-dimensional hydrological and a probabilistic infinite slope stability model. The modelling is applied on a sample mountain catchment, located on Sarno Mountains (Campania, southern Italy), and calibrated using physics-based rainfall thresholds derived from the literature. The results obtained under five simulated constant rainfall intensities (2.5, 5, 10, 20 and 40 mm h−1) show an increase of soil pressure head and major failure probability corresponding to stratigraphic and morphological discontinuities, where a soil thickness reduction occurs. The outcomes obtained from modelling match the hypothesis of the formation of lateral throughflow due to the effect of intense rainfall, which leads to the increase of soil water pressure head and water content, up to values of near-saturation, in narrow zones of the slope, such as those of downslope reduction of total soil thickness and pinching out of soil horizons. The approach proposed can be conceived as a further advance in the comprehension of slope hydrological processes at a detailed scale and their effects on slope stability under given rainfall and antecedent soil hydrological conditions, therefore in predicting the most susceptible areas to initiation of rainfall-induced shallow landslides and the related I-D rainfall thresholds. Results obtained demonstrate the occurrence of a slope hydrological response depending on the spatial variability of soil thickness and leading to focus slope instability in specific slope sectors. The approach proposed is conceived to be potentially exportable to other slope environments for which a spatial modelling of soil thickness would be possible.