Bacterial extracellular enzymes play a significant role in the degradation of organic matter in the open ocean. Using artificial fluorogenic substrates, this research highlights potential artefacts in the response of bacterial glucosidase and aminopeptidase to ocean acidification, and the effects of three different acidification techniques. We conclude that fluorogenic substrate degradation is affected by, or alters pH, and bubbling CO₂ may lead to the overestimation of carbohydrate degradation.