In recent years, catchment similarity measures based on flood seasonality have become popular alternatives for identifying hydrologically homogeneous pooling groups used in regional flood frequency analysis. Generally, flood seasonality pooling measures are less prone to errors and are more robust than measures based on flood magnitude data. However, they are also subject to estimation uncertainty resulting from sampling variability. Because of sampling variability, catchment similarity in flood seasonality can significantly deviate from the true similarity. Therefore sampling variability should be directly incorporated in the pooling algorithm to decrease the level of pooling uncertainty. This paper develops a new pooling approach that takes into consideration the sampling variability of flood seasonality measures used as pooling variables. A nonparametric resampling technique is used to estimate the sampling variability for the target site, as well as for every site that is a potential member of the pooling group for the target site. The variability is quantified by Mahalanobis distance ellipses. The similarity between the target site and the potential site is then assessed by finding the minimum confidence interval at which their Mahalanobis ellipses intersect. The confidence intervals can be related to regional homogeneity, which allows the target degree of regional homogeneity to be set in advance. The approach is applied to a large set of catchments from Great Britain, and its performance is compared with the performance of a previously used pooling technique based on the Euclidean distance. The results demonstrate that the proposed approach outperforms the previously used approach in terms of the overall homogeneity of delineated pooling groups in the study area.