|Elevated groundwater nitrate levels are common in drylands, often in excess of WHO guidelines, with concern for human and animal health. In light of recent attempts to identify nitrate sources in the Kalahari this paper presents the first unsaturated zone (USZ) nitrate profiles and recharge rate estimates for the important transboundary Stampriet Basin, alongside the first rainfall chemistry records. Elevated subsurface nitrate reaches 100–250 and 250–525 mg/L NO3–N, with NO3–N/Cl of 4–12, indicating input above evapotranspiration. Chloride mass balance recharge rates range from 4 to 27 mm/y, indicating a vertical movement of these nitrate pulses toward the water table over multi-decadal timescales. These profiles are sampled from dune crests, away from high concentrations of animals and without termite mounds. Given low-density animal grazing is unlikely to contribute consistent spot-scale nitrate over decades, these profiles give an initial estimate of naturally-produced concentrations. This insight is important for the management of the Stampriet Basin and wider Kalahari groundwater. This study expands our knowledge about elevated nitrate in dryland USZs, demonstrating that it can occur as pulses, probably in response to transient vegetation cover and that it is not limited to long-residence time USZs with very limited downward moisture flux (recharge).