Regional-scale groundwater quality degradation from nonpoint source pollution threatens the long-term sustainability of major alluvial aquifer-aquitard systems worldwide. Upscaled models can efficient represent nonpoint source transport, but fail to accurately characterize non-Fickian (anomalous) transport caused by mean flow direction transience. In this study, we demonstrate that hydrogeologic factors explain this failure. Specifically, vertical anisotropy in K and seasonal pumping and recharge in typical alluvial aquifer systems can fundamentally change hydraulic gradients and shift the mean flow direction between mostly horizontal and mostly vertical flow. Detailed 3D flow and transport simulations in a heterogeneous alluvial aquifer under varying mean flow directions indicate that alterations to hydraulic gradients which control the mean flow direction can lead to increasingly non-Fickian transport. Under mostly horizontal flow, diffusion and slow advection dominant low-K facies slow mass transfer rates from low-K material, and preferential flow along connected high-K networks causes increased spatial spreading along the mean flow direction. Conversely, predominantly vertical flow caused by spatially distributed pumping and recharge shifts mass transfer processes in low-K material from diffusion and slow advection dominant to advection dominant, which results in vertically oriented particle trajectories that compactly migrate through high- and low-K facies alike, leading to increasingly Fickian transport. Thus, mean flow direction transience driven by vertical anisotropy in K and seasonal pumping and recharge can create oscillating transport patterns, ranging from persistently non-Fickian to more Fickian. Results illustrate the hydrogeologic factors that explain why upscaled transport models fail to capture non-Fickian effects resulting from mean flow direction transience.