Although in Europe atmospheric deposition of sulphur has decreased considerably over the last decades, groundwater pollution by sulphate may still continue due to pyrite oxidation in the soil as a result of excessive fertilisation. Inflowing groundwater rich in sulphate can change biogeochemical cycling in nutrient-poor wetland ecosystems. Incoming sulphate loads may induce internal eutrophication as well as the accumulation of dissolved sulphide, which is phytotoxic. We, however, argue that upwelling sulphate rich groundwater may also promote the conservation of rare and threatened alkaline fens, since excessive fertilisation and pyrite oxidation also produces acidity, which invokes calcite dissolution, and increased alkalinity and hardness (Ca2+ + Mg2+) of the inflowing groundwater. Our observations in a very species-rich wetland nature reserve show that sulphate is reduced and effectively precipitates as iron sulphides when this calcareous and sulphate rich groundwater flows upward through the organic soil of the investigated nature reserve. Furthermore, we show that sulphate reduction coincides with an increase in alkalinity production, which in our case results in active calcite precipitation in the soil. In spite of the occurring sulphate reduction we found no evidence for internal eutrophication. Extremely low phosphorous concentration in the pore water could be attributed to a high C:P ratio of soil organic matter and co-precipitation with calcite. Our study shows that seepage dependent alkaline fen ecosystems can be remarkably resilient to fertilisation and pyrite oxidation induced groundwater quality changes.