Any hydropower project requires an ample availability of stream flow data. Unfortunately, most of the hydropower projects especially small hydropower projects are conducted on ungauged river and consequently hydrologists have for a longtime used stream flow estimation methods using the mean annual flows to gauge rivers. Unfortunately flow estimation methods which include the ru- noff data method, area ratio method and the correlation flow methods employ a lot of assumptions which affect their uncertainty. This study was conducted on Bua River in Malawi to unveil the un- certainties of these flow estimation methods. The study was done on a well gauged catchment in order to highlight the variations between the observed, true stream flows and the estimated stream flows for uncertainty analysis. After regionalizing the homogenous sites, catchments using L-moments, an uncertainty analysis was done which showed that the area method is better fol- lowed by the correlating flow method and lastly the runoff data method in terms of bias, accuracy and uncertainty.