Ocean temperatures are rising; species are shifting poleward, and pH is falling (ocean acidification, OA). We summarise current understanding of OA in the brackish Baltic-Skagerrak System, focussing on the direct, indirect and interactive effects of OA with other anthropogenic drivers on marine biogeochemistry, organisms and ecosystems. Substantial recent advances reveal a pattern of stronger responses (positive or negative) of species than ecosystems, more positive responses at lower trophic levels and strong indirect interactions in food-webs. Common emergent themes were as follows: OA drives planktonic systems toward the microbial loop, reducing energy transfer to zooplankton and fish; and nutrient/food availability ameliorates negative impacts of OA. We identify several key areas for further research, notably the need for OA-relevant biogeochemical and ecosystem models, and understanding the ecological and evolutionary capacity of Baltic-Skagerrak ecosystems to respond to OA and other anthropogenic drivers.