The self-potential (SP) method is sensitive to water fluxes in saturated and partially saturated porous media, such as those associated with rainwater infiltration and groundwater recharge. We present a field-based study at the Voulund agricultural test site, Denmark, that is, to the best of our knowledge, the first to focus on the vertical self-potential distribution prior to and during a saline tracer test. A coupled hydrogeophysical modeling framework is used tosimulate the SP response to precipitation and saline tracer infiltration. A layered hydrological model is first obtained by inverting dielectric and matric potential data. The resulting model that compares favorably with electrical resistance tomography models is subsequently used to predict the SP response. The electrokinetic contribution (caused by water fluxes in a charged porous soil) is modeled by an effective excess charge approach that considers both water saturation and pore water salinity. Our results suggest that the effective excess charge evolution prior to the tracer injection is better described by a recent flux-averaged model based on soil water retention functions than by a previously proposed volume-averaging model. This is the first time that raw (i.e., without post-processing or data-correction) vertically distributed SP measurements have been explained by a physically based model. The electrokinetic contribution cannot alone reproduce the experimental SP data during the tracer test and an electro-diffusive contribution (caused by concentration gradients) is needed. The predicted amplitude of this contribution is too small to perfectly explain the data, but the shape is in accordance with the field data. This discrepancy is attributed to imperfect descriptions of electro-diffusive phenomena in partially saturated soils, unaccounted soil heterogeneity, and discrepancies between the measured and predicted electrical conductivities in the tracer infiltration area. This study opens the way for detailed long-term field-based investigations of the SP method in vadose zone hydrology.