A three‐dimensional variable aperture fracture network model for flow and transport in fractured rocks was developed. The model generates both the network of fractures and the variable aperture distribution of individual fractures in the network. Before solving for the flow and transport of the whole network, a library of single‐fracture permeabilities and particle transport residence time spectra is first established. The spatially varying aperture field within an individual fracture plane is constructed by geostatistical methods. Then the flow pattern, the fracture transmissivity, and the residence times for transport of particles through each fracture are calculated. The library of transmissivities and frequency distributions of residence times is used for all fractures in the network by a random selection procedure. The solution of flow through the fracture network and the particle‐tracking calculation of solute transport for the whole network are derived from one side of the network to the other. The model thus developed can handle flow and transport from the single‐fracture scale to the multiple‐fracture scale. The single‐fracture part of the model is consistent with earlier laboratory tests and field observations. The multiple‐fracture aspect of the model was verified in the constant aperture fracture limit with an earlier code. The simulated breakthrough curves obtained from the model display dispersion on two different scales as has been reported from field experiments.