Eggs of the Western spadefoot toad reached 100% mortality in all 29 clutches deposited at a pH below 5.0 in a temporary pond of the Doñana National Park (SW Spain) throughout the wet season of 2006–2007. A similar trend was detected in a neighbouring pond. The proximity of these two ponds to a groundwater pumping area, led to elucidate the possible links between the reduction in pond hydroperiod over past decades (1989–2008) and the decrease of groundwater pH-buffering capacity. The average hydroperiod had decreased by 4 months since 1998–99 in the pond where the extensive egg mortality had occurred. The total alkalinity, and the Mg2+concentration, had also significantly declined in the shallow water-table since 1998–99. This decline of the shallow groundwater buffering capacity could turn this pond more susceptible to the inorganic acidity associated with pyrite oxidation, as the sediment S content was often above 0.03%. The initial ratio of S/Ca + Mg in the summer dry sediment was a good predictor of pore-water pH on re-wetting after desiccation. Therefore, this ratio can give some anticipation to mitigate the impact of acidity on toad hatching before these temporary ponds are reflooded on the next wet season. Results suggest that the long-term damage to pond water levels can trigger a potential risk of soil acidification in the presence of iron-sulphide minerals. informacion[at]ebd.csic.es: Serrano et al (2016) Susceptibility to acidification of groundwater-dependent wetlands affected by water level declines, and potential risk to an early-breeding amphibian species. Sci Total Environ http://dx.doi.org/10.1016/j.scitotenv.2016.07.156