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We present a graph-based method to identify primary flow and transport subnetworks in three-dimensional discrete fracture networks (DFNs). The structure of a DFN lends itself to the use of graphs as a coarse-scale representation that retains the multiscale nature of flow and transport through fracture media. We develop a bipartite graph representation that integrates fracture network topology, fracture geometry, and hydraulic properties. We show that the two most common graph-representations of DFNs, vertices representing intersections and vertices representing fractures, are projections of this bipartite graph thereby providing a generalization of previous DFN-graph frameworks. The primary subnetworks in each DFN are identified by running a heuristic algorithm that determines the edge-disjoint shortest paths through the graph which correspond to the regions where the fastest transport occurs. The method does not have any user-defined parameters and terminates in a finite number of steps. The quality of the method is demonstrated by comparing transport simulations on the identified primary subnetwork and full network, which are in good agreement for early and middle times. These estimates of the first passage times can be achieved with close to an order of magnitude reduction of computational expense using the proposed method. [ABSTRACT FROM AUTHOR]