Estuarine organisms are exposed to multiple stressors including large fluctuations in partial pressure of carbon dioxide (PCO2) and concentrations of trace metals such as cadmium (Cd) that can affect their survival and fitness. Ocean acidification due to the increasing atmospheric PCO2 leads to a decrease in pH and shifts in the carbonate chemistry of seawater which can change bioavailability and toxicity of metals. We studied the interactive effects of PCO2 and Cd exposure on metal levels, metabolism and immune-related functions in hemocytes of two ecologically and economically important bivalve species, Mercenaria mercenaria (hard shell clam) and Crassostrea virginica (Eastern oyster). Clams and oysters were exposed to combinations of three PCO2 levels (∼400, 800 and 2000 μatm PCO2, corresponding to the present day conditions and the projections for the years 2100 and 2250, respectively) and two Cd concentrations (0 and 50 μg l−1) in seawater. Following four weeks of exposure to Cd, hemolymph of both species contained similar Cd levels (50–70 μg l−1), whereas hemocytes accumulated intracellular Cd burdens up to 15–42 mg l−1, regardless of the exposure PCO2. Clam hemocytes had considerably lower Cd burdens than those of oysters (0.7–1 ng 10−6 cells vs. 4–6 ng 10−6 cells, respectively). Cd exposure suppressed hemocyte metabolism and increased the rates of mitochondrial proton leak in normocapnia indicating partial mitochondrial uncoupling. This Cd-induced mitochondrial uncoupling was alleviated in hypercapnia. Cd exposure suppressed immune-related functions in hemocytes of clams and oysters, and these effects were exacerbated at elevated PCO2. Thus, elevated PCO2 combined with Cd exposure resulted in decrease in phagocytic activity and adhesion capacity as well as lower expression of mRNA for lectin and heat shock protein (HSP70) in clam and oyster hemocytes. In oysters, combined exposure to elevated PCO2 and Cd also led to reduced activity of lysozyme in hemocytes and hemolymph. Overall, our study shows that moderately elevated PCO2 (∼800–2000 μatm PCO2) potentiates the negative effects of Cd on immunity and thus may sensitize clams and oysters to pathogens and diseases during seasonal hypercapnia and/or ocean acidification in polluted estuaries.