The aim of this paper is to assess the hydrological system of the Okavango headwater tributaries, namely the Cuito and Cubango sub-catchments, and the flow characteristics of the Okavango after their confluence at Mukwe. This assessment was applied at several gauging stations in the Cubango River reaching from the station Chinhama in Angola down to the station Rundu in Namibia and for two gauging stations (Cuito Cuanavale and Dirico) in the Cuito River system. Identifying hydrological flow characteristics by analysing time series discharge data in terms of frequency, low and peak flow events, and upstream downstream linkages in the mentioned tributaries was supported by the analysis of spatially distributed climate time series and basin characteristics. The analysis of the existing datasets in this data scarce region revealed that the headwater catchments are different in runoff generation, river bed morphology, and storage capacities. The amount of delivered discharge from the Cubango is more varied in amplitude and frequency compared to the more base flow dominated Cuito discharge. Analysing spatial datasets indicated significant differences in natural landscape system features leading to different runoff generation, from fast discharge hydrographs (Cubango) to base flow driven flow dynamics (Cuito). Compiled data as well as assessed hydrological dynamics will allow for the follow-up application of process based J2000 and J2000-g hydrological models for water balance assessment and river basin rainfall-runoff modelling. Keywords: Cubango River, Cuito River, flow duration curves, hydrological assessment, Okavango catchment, upstream-downstream analysis.