This data set presents data from 2 month-long laboratory experiments conducted at GEOMAR, Kiel (Germany) where seawater bicarbonate ion concentrations were manipulated to investigate the effects of limited seawater carbon availability on calcification rates in juvenile Baltic Sea Mytilus edulis trossulus. Calcification rates (mass of calcium carbonate produced per unit time) was measured in 4 replicate tanks across 3 salinities and 5 bicarbonate ion concentrations to estimate the concentration at which bicarbonate ions start to limit calcification in the Baltic Sea at low salinities.