This paper presents a comparative analysis of three partitioning methods, including Fast Greedy, Random Walk, and Metis, which are commonly used to establish the district metered areas (DMAs) in water distribution systems. The performance of the partitioning methods is compared using a spectrum of evaluation indicators, including modularity, conductance, density, expansion, cuts, and communication volume, which measure different topological characteristics of the complex network. A complex water distribution network EXNET is used for comparison considering two cases, i.e., unweighted and weighted edges, where the weights are represented by the demands. The results obtained from the case study network show that the Fast Greedy has a good overall performance. Random Walk can obtain the relative small cut edges, but severely sacrifice the balance of the partitions, in particular when the number of partitions is small. The Metis method has good performance on balancing the size of the clusters. The Fast Greedy method is more effective in the weighted graph partitioning. This study provides an insight for the application of the topology-based partitioning methods to establish district metered areas in a water distribution network.