The nitrate concentration in the subsoil moisture of the vadose zone is an important indicator for future groundwater quality, which is classically determined via centrifugation. Batch extraction is an inexpensive and easy alternative method, but whether these methods measure the same soil water, nitrogen species, and nitrate concentrations is unclear, in particular for loess soils. Two experiments were carried out to assess the differences in nitrate and other anion concentrations between centrifugated soil moisture (centrifugated at different speeds and times) and batch extractions (using double-distilled water and 0.01 M CaCl2). Batch extraction resulted in lower nitrate (−20%) and chloride (−15%) concentrations than centrifugation, mainly due to anion exclusion, where soil microporosity controls the contribution of diffusion, denitrification, and leaching processes. Vice versa, batch extraction overestimated the concentration of nutrients that occur as precipitates in or sorb the soil matrix, such as sulphate (+50%) and ammonium (+96%). Batch extractions can only be used as a proxy to determine actual nitrate concentrations of soil water. However, they are useful to monitor changes in nitrate leaching over time in response to (policy) measures taken. They can also be used as “early warning indicator” and to improve the reliability of spatial explicit monitoring networks.