The paper presents a methodology for the utilisation of the Uncertainty analysis based on Monte Carlo simulations for the design of wastewater treatment systems. The special and important case of facultative-ponds design is exemplified. The design is carried out a large number of times, each run with different values of the inputs, randomly selected from uniform distributions within ranges which define the designer's uncertainty with the data. The results are interpreted statistically, giving elements for the selection of more or less conservative designs, according to the resulting effluent quality. The procedure for undertaking a Sensitivity Analysis is also described and exemplified, allowing the designer to concentrate more efforts on a more accurate determination of those inputs found to be significantly important.