The boundaries between terrestrial and aquatic ecosystems, known as critical transition zones (CTZ), are dynamic interfaces for fluxes of water, sediment, solutes, and gases. Moreover, they often support unique or diverse biotas. Soils, especially those of riparian zones, have not been recognized as CTZ even though they play a critical role in regulating the hydrologic pathways of infiltration and leaching, or runoff and erosion, which can cumulatively affect biogeochemical processes and human livelihoods at landscape scales. In this review, we show how the processes that regulate hydrologic fluxes across and through soil CTZ are influenced by the activities of soil biota. Our message is fourfold. First, there are a variety of ways in which soil biodiversity, in terms of richness and dominance, can influence hydrological pathways in soil and thus the transfer of materials from terrestrial to aquatic ecosystems. Second, the influence of soil organisms on these hydrological pathways is very much interlinked with other environmental, soil biophysical, and vegetation factors that operate at different spatial and temporal scales. Third, we propose that the influence of soil biodiversity on hydrological pathways is most apparent (or identifiable), relative to other factors, in situations that lead to the dominance of certain organisms, such as larger fauna. Fourth, soils are buffered against environmental change by biophysical properties that have developed over long periods of time. Therefore, the effects of changes in soil biodiversity on hydrological processes at the ecosystem scale might be delayed and become most apparent in the long term.