||On the basis of interactions between landscape characteristics and precipitation inputs, watersheds respond differently to different climatic inputs. The objective of this study was to quantitatively characterize controls on runoff generation from two first order micro-catchments in the Amazonia region. The study investigated the variation of hydrological signatures at micro-catchment scale and related these to landscape and land cover differences and weather descriptors that control the observed responses. One catchment is a pasture cleared of all natural vegetation in the early 1980s, and the second catchment is a primary tropical forest with minor signs of disturbance. Water levels and meteorological variables were continuously monitored during the study period (December 2012–May 2013). Water level measurements were converted to discharge, evapotranspiration was quantified using Penman–Monteith equation and catchment pedohydrological properties were also determined. During the study period, mean total rainfall was 1200 mm, and direct runoff ratios were 0.29 and 0.12 for the pasture and forest catchments, respectively. Base flow index was relatively high in the forest catchment (0.76) compared with pasture catchment (0.63). Results from this study showed that the pasture catchment had a 35% higher mean stream flow. Analysis of selected individual rainstorm events also showed peak discharges, which were attained much faster in the pasture catchment compared with the forest catchment. At both sites, rainfall-runoff responses were highly dependent on surface and subsurface flow generation. Overland flow was observed in the pasture site during intense rainfall events. The pasture catchment exhibited higher event water contribution than the forest catchment. Findings from this research suggest that shallow lateral pathways play a significant role in controlling runoff generation processes in the forest catchment, whereas infiltration excess runoff generation processes dominate in the pasture catchment. The findings in this study suggest that the conversion of forest to pasture may lead to important changes in runoff generation processes and water storage in these head water catchments. Copyright © 2014 John Wiley & Sons, Ltd.