AbstractWe study how the interplay between fracture aperture heterogeneity and tracer injection mode controls fluid flow and tracer transport in three‐dimensional (3D) discrete fracture networks (DFNs). The direct 3‐D DFN simulations show that tracer injection mode has substantial effects on tracer spreading across all levels of aperture heterogeneity. The key controlling factor for effective transport is the initial Lagrangian velocity distribution, which is determined by the interplay between injection mode and aperture heterogeneity. The fundamental difference between initial Lagrangian velocity distribution and domain‐scale Eulerian velocity distribution plays a vital role in determining anomalous transport. We effectively capture the observed anomalous transport using an upscaled transport model that incorporates initial velocity distribution, stationary velocity distribution, velocity correlation length, and average advective tortuosity. With the upscaled transport model, we accurately capture the evolution of Lagrangian velocity distribution and predict longitudinal spreading in 3‐D DFN.