A mesocosm experiment was conducted to quantify the effects of medium term (5 wk) exposure to acidified seawater on the structure of Nereis virens (Polychaeta) burrows and sediment nutrient fluxes. Worms were exposed to seawater acidified to a pH of 7.3, 6.5 or 5.6 using carbon dioxide (CO₂) gas. These treatments mimicked the effects of either ocean acidification (pH 7.3) or leakage from a sub-seabed CO₂ storage site (pH 6.5 and 5.6). Results from these treatments were compared to those from worms maintained in natural seawater with a pH ≈ 7.9. The experiment showed that the presence and structure of N. virens burrows significantly increased the sediment uptake of nitrate and the release of ammonium, nitrite and silicate. Phosphate flux was unaffected by the presence of burrows. Nutrient flux rates were also significantly affected by changes in seawater acidity. A reduction in seawater pH caused an increase in nitrate uptake and increase in ammonium release, a decrease in nitrite release and a decrease in phosphate uptake. The flux of silicate was unaffected by changes in seawater pH. As changes in acidity had no impact on the size and structure of worm burrows, it was concluded that the impact of seawater pH on nutrient flux was probably due to changes in the microbial communities responsible for nutrient transformations. Whilst this paper demonstrates that leakage from sub-seabed storage would have significant and immediate effects on nutrient cycling, impacts of ocean acidification through atmospheric absorption are less obvious. This paper concludes that ocean acidification could have a significant impact on sediment nutrient flux in coastal and shelf seas as a result of potential changes in the structure and function of bioturbating communities.