The northern Gulf of Mexico (nGoM) experiences seasonal coastal hypoxia due to nutrient enrichment from the Mississippi-Atchafalaya River basin, leading to one of the world’s largest hypoxic zones. In these shallow zones, benthic processes play an essential role in driving/maintaining deoxygenation and acidification of bottom waters. This dataset investigates carbonate dissolution processes in surface sediment interface of the nGoM during hypoxic conditions in summer 2022 as the main acidification feedback mechanism, with a specific focus on the effects of bottom water acidification. Using high-resolution techniques, this study combines pH and O₂ microprofiling (200 μm) with benthic measurements of carbonate system parameters (pH, DIC, TA, Ca²⁺) to assess carbonate dissolution at millimeter-scale resolution. The pH microprofiles reveal significant decrease in the first 3 cm, with pore water pH reaching values of 6.92 at the most hypoxic station. Despite undersaturation with respect to aragonite and occasionally calcite, Ca²⁺ profiles indicate no significant carbonate dissolution, suggesting stability of calcium carbonate in these sediments during the summer. This lack of dissolution, likely influenced by the absence of aragonite, and possible inhibitory effects of dissolved organic carbon and reactive orthophosphate, points to a limited buffering capacity in these sediments. These insights are essential for refining models predicting coastal acidification and hypoxia responses to environmental stressors in the nGoM and similar eutrophic systems.