In the present study, we demonstrate comprehensive three-dimensional breakthrough pollutant advection-dispersion curve predictions throughout the 3D block of a highly heterogeneous fractured aquifer, using a combination of 3D particle-following tracking (P-FT) outputs and channeling theory results, without substantial computations. The P-FT method neglects slow tracer pathways in groundwater, owing to pollutant recirculation and dead-end pathways, when applied to backbones extracted from discrete fracture networks (DFNs), providing a non-exhaustive advection and dispersion solution in a 3D DFN characterized by preferential flow path formation. The combination of proposed models was positively verified at a local scale using a benchmark DFN in a fractured limestone aquifer in Bari (Italy) to evaluate its suitability for use in larger scale simulations with comprehensive DFNs (up to 100,000 fractures). The modeling results were validated using tracer (chlorophyll-A) concentrations obtained from a well-to-well monitoring/injection test. The P-FT simulations to the DFN-extracted backbones helped to instantly generate suitable histograms of the pollutant concentration as a function of time, providing input for the 3D channeling model solution of the tracer advection-dispersion in the rock aquifer. Unlike other Lagrangian or stochastic models, which accommodate the tail of the expected concentration curve, the solution of the proposed model does not require tail improvements because, in groundwater, the advection-dispersion theory helps to explain the complete trend of pollutant spreading, including macro-scale channeling effects. In addition to the dispersion coefficients and Peclet number, the P-FT output provides information on actual 3D particle displacement, i.e., the 3D pollutant plume spreading through the studied aquifer.