Abstract. Understanding of dominant runoff generation processes in the meso-scale Migina catchment (257.4 km 2 ) in southern Rwanda was improved using analysis of hydrometric data and tracer methods. The paper examines the use of hydrochemical and isotope parameters for separating streamflow into different runoff components by investigating two flood events which occurred during the rainy season "Itumba" (March-May) over a period of 2 yr at two gauging stations. Dissolved silica (SiO 2 ), electrical conductivity (EC), deuterium ( 2 H), oxygen-18 ( 18 O), major anions (Cl − and SO 2− 4 ) and major cations (Na + , K + , Mg 2+ and Ca 2+ ) were analyzed during the events. 2 H, 18 O, Cl − and SiO 2 were finally selected to assess the different contributing sources using mass balance equations and end member mixing analysis for two-and three-component hydrograph separation models. The results obtained by applying two-component hydrograph separations using dissolved silica and chloride as tracers are generally in line with the results of three-component separations using dissolved silica and deuterium. Subsurface runoff is dominating the total discharge during flood events. More than 80 % of the discharge was generated by subsurface runoff for both events. This is supported by observations of shallow groundwater responses in the catchment (depth 0.2-2 m), which show fast infiltration of rainfall water during events. Consequently, shallow groundwater contributes to subsurface stormflow and baseflow generation. This dominance of subsurface contributions is also in line with the observed low runoff coefficient values (16.7 and 44.5 %) for both events. Groundwater recharge during the wet seasons leads to a perennial river system. These results are essential for better water resources planning and management in the region, which is characterized by very highly competing demands (domestic vs. agricultural vs. industrial uses).