Ocean acidification may alter the cycling of nitrogen in coastal sediment and so the sediment-seawater nitrogen flux, an important driver of pelagic productivity. To investigate how this perturbation affects the fluxes of NOᵪ¯ (nitrite/nitrate), NH₄⁺ and O₂ , we incubated estuarine sand and subtidal silt in recirculating seawater with a CO₂ -adjusted pH of 8.1 and 7.9. During a 41-day incubation, the seawater kept at pH 8.1 lost 97% of its NOᵪ¯ content but the seawater kept at pH 7.9 lost only 18%. Excess CO₂ increased benthic photosynthesis. In the silt, this was accompanied by a reversal of the initial NOᵪ¯ efflux into influx. The estuarine sand sustained its initial NOᵪ¯ influx but, by the end of the incubation, released more NH₄⁺ at pH 7.9 than at pH 8.1. We hypothesise that these effects share a common cause; excess CO₂ increased the growth of benthic microalgae and so nutrient competition with ammonia oxidising bacteria (AOB). In the silt, diatoms likely outcompeted AOB for NH₄⁺ and photosynthesis increased the dark/light fluctuations in the pore water oxygenation inhibiting nitrification and coupled nitrification/denitrification. If this is correct, then excess CO₂ may lead to retention of inorganic nitrogen adding to the pressures of increasing coastal eutrophication.