Benthic habitats are the largest habitats on Earth, being essential for marine ecosystem functioning. Benthic habitats are particularly vulnerable towards pollution and anthropogenetic influence due to general oligotrophic nature. We, therefore, simulated pollution events involving nitrate and sulphate, in combination with organic carbon. We then observed the microbiota composition the following month. Surprisingly, upon nitrate addition, an abrupt response was observed between two and three weeks after the pollution event. We observed a threefold reduction in species richness, with a dominance of the genus Pseudarchobacter within the Campylobacteriota phylum, concurring with a decrease in nitrification potential and an increase in Dissimilatory Nitrate Reduction to Ammonium (DNRA) and a regain in denitrification. Likewise, addition of sulphate contributed to a delayed response with reduction in species richness albeit weaker than for nitrate, leading to a shift towards potential spore-forming Firmicutes. There was also an increase in DNRA, but only for the oxic conditions, concurring with a regain in sulphate reductio and denitrification. For the nitrate addition experiments, the delay in response could potentially be attributed to the genus Pseudarchobacter which rely on sulphides for denitrification, while for the sulphate addition experiments, the delayed response might be explained by the germination of spores. The late increase of DNRA may indicate a shift towards a different metabolic regime for nitrogen. In conclusion, our microcosm experiments revealed delayed abrupt microbiota shifts resembling tipping points that can potentially be overlooked in natural ecosystems.