The distribution of mussel in estuaries is limited but the mechanisms are not well understood. We document for the first time that reduced Ca²⁺ concentration in the low saline, brackish Baltic Sea affects the ability of mussel larvae to calcify the first larval shell. As complete formation of the shell is a prerequisite for successful development, impaired calcification during this sensitive life stage can have detrimental effects on the species' ability to colonize habitats.