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This work presents a modeling approach for single-phase flow in 3D fractured porous media with non-conforming meshes. To this end, a Lagrange multiplier method is combined with a parallel $L^2$-projection variational transfer approach. This Lagrange multiplier method enables the use of non-conforming meshes and depicts the variable coupling between fracture and matrix domain. The $L^2$-projection variational transfer allows general, accurate, and parallel projection of variables between non-conforming meshes (i.e. between fracture and matrix domain). Comparisons of simulations with 2D benchmarks show good agreement, and the method is further validated on 3D fracture networks by comparing it to results from conforming mesh simulations which were used as a reference. Application to realistic fracture networks with hundreds of fractures is demonstrated. Mesh size and mesh convergence are investigated for benchmark cases and 3D fracture network applications. Results demonstrate that the Lagrange multiplier method, in combination with the $L^2$-projection method, is capable of modeling single-phase flow through realistic 3D fracture networks.