Canopy throughfall comprises the largest portion of net precipitation that is delivered to the forest floor. This water flux is highly variable across space and time and is influenced by species composition, canopy foliage, stand structure, and storm meteorological characteristics. In upland forests throughout the central hardwoods region of the Eastern United States, a compositional shift is occurring from oak-hickory to more mesic, shade-tolerant species such as red maple, sweetgum, and winged elm. To better understand the impacts of this shift on throughfall flux and the hydrologic budget, we monitored throughfall for one year in Northern Mississippi under the crowns of midstory and overstory oak (post oak and southern red oak) and non-oak species (hickory, red maple, and winged elm). In general, oak had more throughfall than co-occurring non-oak species in both canopy levels. In the overstory during the leaf-off canopy phase, white oak had relatively higher throughfall partitioning (standardized z-score = 0.54) compared to all other species (z-score = −0.02) (p = 0.004), while in the leaf-on canopy phase, red maple had relatively lower throughfall (z-score = −0.36) partitioning compared to all other species (z-score = 0.11). In the midstory, red maple was the only species to exhibit a difference in throughfall between canopy phases, with much lower throughfall in the leaf-off compared to the leaf-on canopy phase (z-score = −0.30 vs. 0.202, p = 0.039). Additionally, throughfall under oak crowns was less variable than under non-oak crowns. These results provide evidence that the spatial and temporal distribution of throughfall inputs under oak crowns are different than non-oak species, likely due to differences in crown architecture (i.e., depth and density). As oak dominance diminishes in these forests, it is possible that the portion of rainfall diverted to throughfall may decrease as well. The net impacts to watershed hydrology are still unknown, but these results provide one mechanism by which the distribution of water resources may be affected.