This paper focuses on uncertainty analysis to aid decision making in applications of statistically modeled flow-duration-frequency (FDF) relationships of both daily high and low flows. The analysis is based on 24 selected catchments in the Lake Victoria basin in Eastern Africa. The FDF relationships were derived for aggregation levels in the range 1–90 days for high flows and 1–365 days for low flows. The validity of the projected FDF quantiles for high return periods T was checked using growth factor curves. Monte Carlo simulations were used to construct confidence intervals CI on both the estimated Ts for given flows and the estimated FDF quantiles for given T. The average bias of the modeled T of high and low flows are for all catchments and Ts up to 25 years lower than 8%. Despite this relatively small average bias in the modeled T, the limits of the CI on the modeled 25-year flows go up to more than 100% for high flows and more than 150% for low flows. The assessed FDF relationships and accompanied uncertainties are useful for various types of risk based water engineering and water management applications related to floods and droughts.