Description: It has been speculated that macrophytes beds might act as a refuge for calcifiers from ocean acidification. In the shallow nearshores of the western Kiel Bay (Baltic Sea), mussel and seagrass beds are interlacing, forming a mosaic habitat. Naturally, the diverse physiological activities of seagrasses and mussels are affected by seawater carbonate chemistry and they locally modify it in return. Calcification by shellfishes is sensitive to seawater acidity; therefore the photosynthetic activity of seagrasses in confined shallow waters creates favorable chemical conditions to calcification at daytime but turn the habitat less favorable or even corrosive to shells at night. In contrast, mussel respiration releases CO2, turning the environment more favorable for photosynthesis by adjacent seagrasses. At the end of summer, these dynamics are altered by the invasion of high pCO2/low O2 coming from the deep water of the Bay. However, it is in summer that mussel spats settle on the leaves of seagrasses until migrating to the permanent habitat where they will grow adult. These early life phases (larvae/spats) are considered as most sensitive with regard to seawater acidity. So far, the dynamics of CO2 have never been continuously measured during this key period of the year, mostly due to the technological limitations. In this project we used a combination of state-of-the-art technologies and discrete sampling to obtain high-resolution time-series of pCO2 and O2 at the interface between a seagrass and a mussel patch in Kiel Bay in August and September 2013. From these, we derive the entire carbonate chemistry using statistical models. We found the monthly average pCO2 more than 50 % (approx. 640 μatm for August and September) above atmospheric equilibrium right above the mussel patch together with large diel variations of pCO2 within 24 h: 887 ± 331 μatm in August and 742 ± 281 μatm in September (mean ± SD). We observed important daily corrosiveness for calcium carbonates (Ωarag and Ωcalc 〈 1) centered on sunrise. On the positive side, the investigated habitat never suffered from hypoxia during the study period. We emphasize the need for more experiments on the impact of these acidic conditions on (juvenile) mussels with a focus on the distinct day-night variations observed.