The increase in biogenic carbonate dissolution in coastal sediments is an expected response to current ocean acidification. However, the interaction between the continent, coastal sediments, the atmosphere, and the ocean establishes complex controls on the carbonate system, indicating that ongoing open ocean acidification cannot be directly applied to coastal environments. Understanding the factors influencing the preservation of biogenic carbonates in coastal areas is crucial for carbon cycling, as 50% of these carbonates are found in coastal sediments. This study evaluates carbonate dissolution in permeable sediments across different locations. While attention is given to surface water acidification and its impact over net CaCO₃ dissolution dynamics in sediments, results demonstrate a stronger correlation of CaCO₃ dissolution rates with porewater composition. On average, a pH difference of 0.2 units exists between surface seawater and porewater in the studied sites. Moreover, the arrival of continental groundwater to these systems, forming the so-called subterranean estuaries, further exacerbates the non-dependency of biogenic carbonate stability in relation to carbonate system properties of the overlying waters. The findings also suggest that biogenic carbonate dissolution/precipitation rates are strongly modulated by benthic metabolism and regulated by daily light-dark cycles. During daylight hours, net calcification dominates, whereas net dissolution occurs in darkness, independently of the pH of the overlying water. Metabolic respiration rates from various studies exhibit moderate positive correlations with dissolution rates in the darkness, whereas the relationship between net primary production (NPP) and dissolution in light conditions vanishes. Continental groundwater commonly transports land-derived carbonate system properties and, depending on its composition, can promote pH decline and calcium carbonate undersaturation, thereby promoting carbonate dissolution. Benthic metabolism along the continental groundwater flow path and within the subterranean estuary also contributes to the variation in porewater pH, further shaping the carbonate system of the local porewaters and benthic CaCO₃ stability.