Hydrological models are widely used tools in water resources estimation, but they are simple representations of reality and are frequently based on inadequate input data and uncertainties in parameter values. Data observation networks are expensive to establish and maintain and often beyond the resources of most developing countries. Consequently, measurements are difficult to obtain and observation networks in many countries are shrinking, hence obtaining representative observations in space and time remains a challenge. This study presents some guidelines on the identification, quantification and reduction of sources of uncertainty in water resources estimation in southern Africa, a data scarce region. The analyses are based on example sub-basins drawn from South Africa and the application of the Pitman hydrological model. While it has always been recognised that estimates of water resources availability for the region are subject to possible errors, the quantification of these uncertainties has never been explicitly incorporated into the methods used in the region. The motivation for this study was therefore to contribute to the future development of a revised framework for water resources estimation that does include uncertainty. The focus was on uncertainties associated with climate input data, parameter estimation (and recognizing the uncertainty due model structure deficiencies) methods and water use data. In addition to variance based measures of uncertainty, this study also used a reservoir yield based statistic to evaluate model output uncertainty, which represents an integrated measure of flow regime variations and one that can be more easily understood by water resources managers. Through a sensitivity analysis approach, the results of the individual contribution of each source of uncertainty suggest regional differences and that clear statements about which source of uncertainty is likely to dominate are not generally possible. Parameter sensitivity analysis was used in identifying parameters which are important withinspecific sub-basins and therefore those to focus on in uncertainty analysis. The study used a simple framework for evaluating the combined contribution of uncertainty sources to model outputs that is consistent with the model limitations and data available, and that allows direct quantitative comparison between model outputs obtained by using different sources of information and methods within Spatial and Time Series Information Modelling (SPATSIM) software. The results from combining the sources of uncertainties showed that parameter uncertainty dominates the contribution to model output uncertainty. However, in some parts of the country especially those with complex topography, which tend to experience high rainfall spatial variability, rainfall uncertainty is equally dominant, while the contributions of evaporation and water use data uncertainty are relatively small. While the results of this study are encouraging, the weaknesses of the methods used to quantify uncertainty (especially subjectivity involved in evaluating parameter uncertainty) should not be neglected and require further evaluations. An effort to reduce data and parameter uncertainty shows that this can only be achieved if data access at appropriate scale and quality improves. Perhaps the focus should be on maintaining existing networks and concentrating research efforts on making the most out of the emerging data products derived from remote sensing platforms. While this study presents some initial guidelines for evaluating uncertainty in South Africa, there is need to overcome several constraints which are related to data availability and accuracy, the models used and the capacity or willingness to adopt new methods that incorporate uncertainty. The study has provided a starting point for the development of new approaches to modelling water resources in the region that include uncertain estimates.