Ammonia oxidation is a key microbial process within the marine N-cycle. Sediment and water column samples from two contrasting sites in the English Channel (mud and sand) were incubated (up to 14 weeks) in CO2-acidified seawater ranging from pH 8.0 to pH 6.1. Additional observations were made off the island of Ischia (Mediterranean Sea), a natural analogue site, where long-term thermogenic CO2 ebullition occurs (from pH 8.2 to pH 7.6). Water column ammonia oxidation rates in English Channel samples decreased under low pH with near-complete inhibition at pH 6.5. Water column Ischia samples showed a similar though not statistically significant trend. However, sediment ammonia oxidation rates at all three locations were not affected by reduced pH. These observations may be explained by buffering within sediments or low-pH adaptation of the microbial ammonia oxidizing communities. Our observations have implications for modeling the future impact of ocean acidification on marine ecosystems.