Upscaled transport models are needed to address regional-scale groundwater quality degradation in major aquifers worldwide, and these models must accurately characterize anomalous (non-Fickian) transport (e.g., early solute arrival due to preferential flow, and late time tailing). Although it is well known that seasonal pumping and recharge can cause vertical hydraulic gradient values to exceed horizontal gradients by 10-100 times, the relationship between large shifts in vertical to horizontal gradient ratio (VHGR) and plume migration is less understood. We simulate flow and transport of a conservative solute in a heterogeneous alluvial aquifer under varying VHGR representative of typical seasonal hydraulic gradient fluctuations and find that VHGR strongly impacts anomalous transport, plume migration, and mass transfer rates between hydrofacies. At low VHGR (e.g., ambient hydraulic gradient conditions corresponding to a more horizontal flow direction), low-K facies are diffusion-dominated, resulting in low mass transfer rates out of low-K material, increased spatial spreading along the mean flow direction, and tortuous particle trajectories. In contrast, at high VHGR (e.g., representative of pumping and recharge, and corresponding to an increasingly vertical mean flow direction), results in increasingly Fickian transport, explained by a shift from diffusion- to advection-dominated mass transfer in low-K facies, and illustrated by relatively non-tortuous, vertically oriented particle trajectories. We conclude that seasonal fluctuations in VHGR in a typical alluvial aquifer system may create oscillating transport behavior, with implications for contaminant transport and cleanup. The strong dependence of anomalous transport on VHGR implies that approaches to upscale anomalous transport may benefit from incorporating information about the VHGR, and highlights specific hydrogeologic forcings that cause upscaled transport methods to fail under transient boundary conditions.