Fractures in porous media have been documented extensively. However, they are often omitted from groundwater flow and mass transport models due to a lack of data on fracture hydraulic properties and the computational burden of simulating fractures explicitly in large model domains. We present a MATLAB toolbox, FracKfinder, that automates HydroGeoSphere (HGS), a variably-saturated, control volume finite-element model, to simulate an ensemble of discrete fracture network (DFN) flow experiments on a single cubic model mesh containing a stochastically-generated fracture network. Because DFN simulations in HGS can simulate flow in both a porous media and a fracture domain, this toolbox computes tensors for both the matrix and fractures of a porous medium. Each model in the ensemble represents a different orientation of the hydraulic gradient, thus minimizing the likelihood that a single hydraulic gradient orientation will dominate the tensor computation. Linear regression on matrices containing the computed 3-D hydraulic conductivity (K) values from each rotation of the hydraulic gradient is used to compute the K tensors. This approach shows that the hydraulic behavior of fracture networks can be simulated where fracture hydraulic data are limited. Simulation of a bromide tracer experiment using K tensors computed with FracKfinder in HydroGeoSphere demonstrates good agreement with a previous large-column, laboratory study. The toolbox provides a potential pathway to upscale groundwater flow and mass transport processes in fractured media to larger scales.