The transboundary region of the Iishana system in the western Cuvelai Basin, between southern Angola and northern Namibia, is frequently affected by floods at irregular intervals. As a result, the predominantly rural, subsistence farming population experienced crop failures, human and economic losses. To date, very little is known about the generation of floods, flood concentration, and stormwater drainage dynamics in this region. Therefore, in order to intensively study the runoff behavior and interconnectivity of the Iishana system, 2D-hydrodynamic modeling was used to reconstruct one of the latest major flood events during the rainy season from November 2008 to March 2009. The model focused on the eastern part of the Iishana system, which was most affected by floods and flood damage due to the high population density in and around Oshakati, the regional capital. Two main streams were identified noteworthy because they merge and subsequently affect Oshakati. Water depths vary from 0.1 m to 14 m, with an average of 0.2 m, while water depths above 5 m were attributed to borrow pits. The inundation area ranged up to 1,860 km² and the amount of water left after the rainy season was determined between 0.116 km³ and 0.547 km³, depending on the amount of evapotranspiration (ET) considered in the model. Thus, in the Angolan part of the Iishana system, significantly larger quantities of water are available for longer periods of time during the subsequent dry season, whereas the system in Namibia stores less water, resulting in a shorter water retention period.