The occurrence of rainfall-induced slope failures has become more frequent due to the effect of climate change. Hence, various studies have been conducted to analyse the effect of rainfall infiltration on slope stability. Physically-based hydrological models have been commonly used with slope stability models such as the infinite slope model to develop slope susceptibility maps. However, a combination of three-dimensional (3D) water balance model with 3D limit equilibrium method (LEM) has not been commonly used. Hence, in this study, a water balance model, GEOtop was used to investigate the influence of subsurface flow in unsaturated soil under extreme rainfall conditions on regional slope stability in 3D directions. The results from the GEOtop model were used as inputs for 3D LEM slope stability analysis performed using the Scoops3D software to obtain the factor of safety (FOS) map for the region. Four slopes within the region were then selected to be modelled in the two-dimensional (2D) seepage and slope stability analyses, SEEP/W and SLOPE/W. Results from the detailed study showed that the pore-water pressures (PWPs) from the 3D water balance analyses were found to be higher than the 2D seepage analyses. Under similar PWP conditions, the FOS from the 2D slope stability analysis was observed to be lower than the 3D analysis for two out of the four slopes. However, the combined 3D water balance and slope stability analyses produced lower FOS compared to the 2D seepage and slope stability analyses due to the higher PWPs in the 3D water balance analyses. Therefore, this study highlights the importance of considering the 3D subsurface flow in unsaturated soil given that it has a significant influence on the FOS of slopes.