Anthropogenic CO2 emissions are rapidly changing seawater temperature, pH and carbonate chemistry. This study compares the embryonic development under high pCO2 conditions across the south-north distribution range of the marine clam Limecola balthica in NW Europe. The combined effects of elevated temperature and reduced pH on hatching success and size varied strongly between the three studied populations, with the Gulf of Finland population appearing most endangered under the conditions predicted to occur by 2100. These results demonstrate that the assessment of marine faunal population persistence to future climatic conditions needs to consider the interactive effects of co-occurring physico-chemical alterations in seawater within the local context that determines population fitness, adaptation potential and the system resilience to environmental change.