- Summary For 25 years, a plant in Israel manufacturing ammonium perchlorate disposed of untreated wastewater in four unlined ponds. This study explores the transport mechanisms of perchlorate infiltrated from 1965 to 1990 from one of these active storage ponds into a deep (40 m) layered vadose zone and the underlying Israeli coastal aquifer. Perchlorate migration from 1990, when wastewater disposal ceased, until today, with infiltration due only to natural rain (∼500 mm y −1 ), was also studied. Several indirect methods were used, including: mass balance in the unsaturated zone profile, δ 18 O and δ 2 H profiles below the pond, and a comparison of the same sediment profiles in 2005 and 2007. The isotopic composition of the pore water could be divided into two separate groups: lighter (depleted) and heavier (enriched) samples. All samples in the lighter group were from the shallow vadose zone, above two clayey layers, and represent natural infiltration of rainwater. The enriched samples were from the deeper section of the unsaturated zone (20–40 m) and represent water used for perchlorate manufacturing 14 years prior to drilling. Consequently, the overall maximum infiltration rate was estimated to be 1.4 m y −1 . Below the clayey layer almost identical perchlorate concentrations were found along the sediment profile in 2005 and 2007 (two boreholes, 3 m apart). Very different perchlorate profiles were observed above the clayey layers. This suggests that perchlorate below the clay layers (20–40 m) is practically stagnant under the current natural conditions. The reduction in perchlorate concentration in groundwater below the ponds vs. its increased concentration further downgradient supports the contention that the current migration of perchlorate from the vadose zone to the groundwater is very small. We estimate that perchlorate concentration in the groundwater under the infiltration pond, which was 187 mg l −1 in 2004, will reach 10 μg l −1 within about 14 years. The existence of a clayey layer crossing the thick vadose zone was thus found to significantly change the infiltration rate when ponded conditions were replaced with natural precipitation.