Invasive trees in catchments around the world are a source of concern due to their hydrological and ecological impacts. A large number of studies have focused on their impact on dry-season stream discharge due to enhanced transpiration. The impact of invasive trees on stream discharge and flood risk during extreme rain events, which are becoming more frequent due to climate change, has not been addressed adequately. We examined the influence of land-cover, canopy cover, and other catchment morphological characteristics on stream discharges in hilly catchments during light, heavy, and extreme rain events. Three years of rainfall-runoff observations, between January 2014 and December 2016, were collected in eleven neighbouring mountainous catchments in Nilgiris, South India. Each catchment had a distinct land cover, namely shola forests, montane grasslands, and catchments invaded by wattle (Acacia mearnsii). Hourly rain intensities between the percentiles 25–90, 90–95 and over 95 were categorised as light, heavy and extreme respectively, and were used to study hourly peak stream discharge responses. We compared discharge between native grassland catchments and grassland catchments invaded by wattle. Discharge rates were corrected for the catchment area. We found that land cover and canopy-cover influenced the hydrologic response to extreme rain events. Regression models with flood event as the response variable suggested an increase in rainfall-runoff response with an increase in canopy cover. The maximum hourly discharge observed in the reference grassland catchment (0.00098 mm s−1) was lower than the maximum discharge observed in low density (0.00529 mm s−1) and high density (0.00497 mm s−1) wattle catchments. At higher discharges, the flood magnitude in wattle invaded catchments was much greater than that in the grassland catchment for a given flood frequency – indicating a higher risk of severe flooding in wattle-dominated catchments. We attribute the enhanced flood discharges to the effects of spreading wattle roots on the enhancement of rapid, shallow sub-surface flows in invaded catchments. Catchments dominated by shallow sub-surface flows are known to have reduced water retention times in response to high rain intensities. Antecedent moisture conditions and drainage density were other factors that influenced the local rainfall-runoff relationships. In the Western Ghats and other parts of India grasslands have been planted with exotic woody trees, and some have become invasive. Our study indicates that replacing grasslands with woody plants at landscape scales, could affect hydrological processes and could increase flood risks during the monsoon, especially in mountainous regions. Management of invaded catchments by regulation of wattle and restoration of semi-natural grassland, combined with the installation of early warning systems in these impacted areas will help reduce flood risk during extreme rain under climate change.