This research incorporates the generalized likelihood uncertainty estimation (GLUE) methodology in a high-resolution Environmental Protection Agency Storm Water Management Model (SWMM), which we developed for a highly urbanized sewershed in Syracuse, NY, to assess SWMM modelling uncertainties and estimate parameters. We addressed two issues that have long been suggested having a great impact on the GLUE uncertainty estimation: the observations used to construct the likelihood measure and the sampling approach to obtain the posterior samples of the input parameters and prediction bounds of the model output. First, on the basis of the Bayes' theorem, we compared the prediction bounds generated from the same Gaussian distribution likelihood measure conditioned on flow observations of varying magnitude. Second, we employed two sampling techniques, the sampling importance resampling (SIR) and the threshold sampling methods, to generate posterior parameter distributions and prediction bounds, based on which the sampling efficiency was compared. In addition, for a better understanding of the hydrological responses of different pervious land covers in urban areas, we developed new parameter sets in SWMM representing the hydrological properties of trees and lawns, which were estimated through the GLUE procedure. The results showed that SIR was a more effective alternative to the conventional threshold sampling method. The combined total flow and peak flow data were an efficient alternative to the intensive 5-min flow data for reducing SWMM parameter and output uncertainties. Several runoff control parameters were found to have a great effect on peak flows, including the newly introduced parameters for trees. Copyright © 2013 John Wiley & Sons, Ltd.