Chloride mass balance (CMB) is used routinely to estimate recharge in arid and semi-arid environments. We tested the CMB method in low chloride environments, when pore waters were <5 mg/L, and found significant errors. The resulting recharge estimates were consistently low by factors of 5 or more. In some cases, oven drying was found to increase the estimated pore-water chloride concentrations, possibly due to enhanced mineral release. Where pore water was extracted by centrifugation, anion exclusion increased the chloride concentrations, often by a factor of 5 or more. Precautions are required when using CMB to estimate recharge whenever the chloride concentrations are low and recharge rates are above a few mm per year.