Coastal vegetated ecosystems are being increasingly recognized for their capacity to capture carbon, provide long-term biogenic storage, and alleviate nutrient pollution. To assess the ability of shallow, vegetated coastal bays to function as blue carbon and nutrient (nitrogen and phosphorus) sinks, we collected sediment cores in nine shallow enclosed bays (representative of the EU Habitats 1153 and 1154) in the archipelago areas of Sweden (Stockholm), Åland Island, and southwestern Finland. Our study showed strong uniformity of carbon and nutrient storage, substantial accumulation of carbon and nutrients, and minimal regional differences in carbon, nitrogen, and phosphorus sediment stocks. These findings are noteworthy given the large area (142 km2) the shallow enclosed bays cover and the multiple important ecosystem services they provide in the northern Baltic Sea seascape. An initial first-order estimate for the shallow bay ecosystems across the study region indicates that these ecosystems potentially store 84,000 to 430,000 t organic carbon over the top 25 cm sediment. The positive correlation between carbon and nitrogen stocks, and the potentially organically bound nature of phosphorus in sediment, suggests that climate regulation services can be managed in unison with nutrient management efforts. The findings, also considering the consistent pattern of slow sedimentation and accumulation, underscore the importance of protecting shallow coastal bays as carbon and nutrient sinks in the Baltic Sea region.