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<p>The Baltic Sea has a salinity gradient decreasing from fully marine (<span class="inline-formula">&gt;</span> 25) in the west to below 7 in the central Baltic Proper. Habitat-forming and ecologically dominant mytilid mussels exhibit decreasing growth when salinity <span class="inline-formula">&lt;</span> 11; however, the mechanisms underlying reduced calcification rates in dilute seawater are not fully understood. Both [HCO<span class="inline-formula"><math xmlns="http://www.w3.org/1998/Math/MathML" id="M3" display="inline" overflow="scroll" dspmath="mathml"><mrow><msubsup><mi/><mn mathvariant="normal">3</mn><mo>-</mo></msubsup></mrow></math><span><svg:svg xmlns:svg="http://www.w3.org/2000/svg" width="9pt" height="16pt" class="svg-formula" dspmath="mathimg" md5hash="0aaab3ee324d7a9ba8e4b96f67d8036e"><svg:image xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="bg-18-2573-2021-ie00001.svg" width="9pt" height="16pt" src="bg-18-2573-2021-ie00001.png"/></svg:svg></span></span>] and [Ca<span class="inline-formula">²⁺</span>] also decrease with salinity, challenging calcifying organisms through CaCO<span class="inline-formula">₃</span> undersaturation (<span class="inline-formula">Ω≤1</span>) and unfavourable ratios of calcification substrates ([Ca<span class="inline-formula">²⁺</span>] and [HCO<span class="inline-formula"><math xmlns="http://www.w3.org/1998/Math/MathML" id="M8" display="inline" overflow="scroll" dspmath="mathml"><mrow><msubsup><mi/><mn mathvariant="normal">3</mn><mo>-</mo></msubsup></mrow></math><span><svg:svg xmlns:svg="http://www.w3.org/2000/svg" width="9pt" height="16pt" class="svg-formula" dspmath="mathimg" md5hash="7de8959157e6c258409d4c11688ca166"><svg:image xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="bg-18-2573-2021-ie00002.svg" width="9pt" height="16pt" src="bg-18-2573-2021-ie00002.png"/></svg:svg></span></span>]) to the inhibitor (H<span class="inline-formula">⁺</span>), expressed as the extended substrate–inhibitor ratio (ESIR). This study combined in situ monitoring of three southwest Baltic mussel reefs with two laboratory experiments to assess how various environmental conditions and isolated abiotic factors (salinity, [Ca<span class="inline-formula">²⁺</span>], [HCO<span class="inline-formula"><math xmlns="http://www.w3.org/1998/Math/MathML" id="M11" display="inline" overflow="scroll" dspmath="mathml"><mrow><msubsup><mi/><mn mathvariant="normal">3</mn><mo>-</mo></msubsup></mrow></math><span><svg:svg xmlns:svg="http://www.w3.org/2000/svg" width="9pt" height="16pt" class="svg-formula" dspmath="mathimg" md5hash="fa1148a5a7ab62133104fb46bf612014"><svg:image xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="bg-18-2573-2021-ie00003.svg" width="9pt" height="16pt" src="bg-18-2573-2021-ie00003.png"/></svg:svg></span></span>] and pH) impact calcification in mytilid mussels along the Baltic salinity gradient. Laboratory experiments rearing juvenile Baltic <i>Mytilus</i> at a range of salinities (6, 11 and 16), HCO<span class="inline-formula"><math xmlns="http://www.w3.org/1998/Math/MathML" id="M12" display="inline" overflow="scroll" dspmath="mathml"><mrow><msubsup><mi/><mn mathvariant="normal">3</mn><mo>-</mo></msubsup></mrow></math><span><svg:svg xmlns:svg="http://www.w3.org/2000/svg" width="9pt" height="16pt" class="svg-formula" dspmath="mathimg" md5hash="ee54bb0fff66afdafaf51bed1fde360d"><svg:image xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="bg-18-2573-2021-ie00004.svg" width="9pt" height="16pt" src="bg-18-2573-2021-ie00004.png"/></svg:svg></span></span> concentrations (300–2100 <span class="inline-formula">µ</span>mol kg<span class="inline-formula">⁻¹</span>) and Ca<span class="inline-formula">²⁺</span> concentrations (0.5–4 mmol kg<span class="inline-formula">⁻¹</span>) reveal that as individual factors, low [HCO<span class="inline-formula"><math xmlns="http://www.w3.org/1998/Math/MathML" id="M17" display="inline" overflow="scroll" dspmath="mathml"><mrow><msubsup><mi/><mn mathvariant="normal">3</mn><mo>-</mo></msubsup></mrow></math><span><svg:svg xmlns:svg="http://www.w3.org/2000/svg" width="9pt" height="16pt" class="svg-formula" dspmath="mathimg" md5hash="5a2143864edd3f7cf8f1639018917994"><svg:image xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="bg-18-2573-2021-ie00005.svg" width="9pt" height="16pt" src="bg-18-2573-2021-ie00005.png"/></svg:svg></span></span>], pH and salinity cannot explain low calcification rates in the Baltic Sea. Calcification rates are impeded when <span class="inline-formula">Ω_aragonite</span> <span class="inline-formula">≤</span> 1 or ESIR <span class="inline-formula">≤</span> 0.7 primarily due to [Ca<span class="inline-formula">²⁺</span>] limitation which becomes relevant at a salinity of ca. 11 in the Baltic Sea. Field monitoring of carbonate chemistry and calcification rates suggest increased food availability may be able to mask the negative impacts of periodic sub-optimal carbonate chemistry, but not when seawater conditions are permanently adverse, as observed in two Baltic reefs at salinities <span class="inline-formula">&lt;</span> 11. Regional climate models predict a rapid desalination of the southwest and central Baltic over the next century and potentially a reduction in [Ca<span class="inline-formula">²⁺</span>] which may shift the distribution of marine calcifiers westward. It is therefore vital to understand the mechanisms by which the ionic composition of seawater impacts bivalve calcification for better predicting the future of benthic Baltic ecosystems.</p>