Abstract The streamline based technology has proven to be effective for various subsurface flow and transport modeling problems including reservoir simulation, model calibration and optimization. For naturally fractured systems, current streamline models are well suited for dual porosity single permeability systems because streamlines need to be traced only for the fracture system. However, complications arise for dual porosity dual permeability (DPDP) systems because streamlines need to be traced for both fracture and matrix systems. Also, the streamlines in the two systems may interact. We present a robust streamline tracing framework for use in the DPDP models via an embedded discrete fracture model (EDFM) framework. The EDFM models utilize irregular gridding and non-neighbor connections to explicitly represent the discrete facture network. Our strategy is based on a boundary layer method that can be used to honor the fluxes at the matrix-fracture interface during streamline tracing. We generalize our previously proposed streamline tracing algorithms for local grid refinements (LGR) and faulted systems to discrete fracture network models where a fracture gridblock in EDFM is treated as a boundary layer for flux continuity and streamline tracing. The proposed method is benchmarked with a semi-analytical solution and a series of numerical examples encompassing different levels of geologic and geometrical complexity to illustrate the accuracy and robustness of the approach. Visualization of streamlines in complex fracture networks provide flow diagnostics such as sweep efficiency and connectivity of wells and fractures. The streamlines are then utilized to develop a workflow for rate allocation optimization for waterflood in naturally fractured reservoirs. We utilized a streamline-based gradient free algorithm whereby both injection and production rates are adjusted under realistic operational constraints. This approach only requires a few forward simulations and therefore offers significant advantages in terms of computational efficiency. It is confirmed that the optimized schedule provides improvements in oil recovery and sweep efficiency compared to the base scenario with uniform injection and production rates. The uniqueness of this work is the robust streamline tracing algorithm in the EDFM using a novel boundary layer based approach for flux continuity. The proposed approach is simple and easy to implement and can be coupled with commercial simulators for field scale applications.