Years of slash-and-burn activities across the tropics have led to very a patchy land-cover with vegetation in various stages of regrowth but, the associated effects on runoff generation remain under-studied. We analysed soil moisture-, perched water level- and overland flow (OF) dynamics during two periods (15 February–2 November 2015 and 20 December 2015–2 March 2016) for plots in a small catchment in Eastern Madagascar where slash-and-burn agriculture has been practiced for more than 50 years: a 1.58 ha tree fallow (TF2), a 1.93 ha terraced shrub fallow (TSF), and a 0.08 ha degraded grassland plot with regularly coppiced and burned eucalypt trees (EUC). Near-surface saturated soil hydraulic conductivity (Ksat) was distinctly lower beneath TF2 compared to TSF and EUC, leading to distinctly different perched water level responses and OF occurrence. OF was highest for TF2 and lowest for TSF. Soil moisture content was lowest for EUC, resulting in the lowest antecedent moisture plus precipitation threshold for OF occurrence (82 mm compared to 129 mm for TSF and 137 mm for TF2). OF was generally in the form of saturation overland flow (SOF) and reflected perched water level dynamics, except at EUC where the occurrence of a perched water level was rare during the first measurement period. Soil moisture responses to rainfall at EUC were highly variable and became larger after harvesting and burning the plot prior to the second measurement period. These results show that soil physical properties and runoff-generation processes in areas with a long history of slash-and-burn agriculture can vary markedly over small spatial scales and need to be taken into account if catchment scale runoff responses are to be simulated or predicted.