Gills of marine bivalves, the organs that mediate water flow for feeding and other physiological functions, are exposed to increasing levels of carbon dioxide (CO₂) in seawater, in response to ocean acidification (OA). We examined the effects of elevated dissolved CO₂ upon filtration and feeding behavior of the blue mussel, Mytilus edulis, under field conditions and in laboratory studies. We further investigated possible changes in cilia beat function in response to elevated dissolved CO₂. Physiological filtration and feeding variables measured; included clearance, filtration, organic ingestion, and assimilation rates and selection efficiency, which decreased with increasing CO₂. Absorption efficiency was not affected by dissolved CO₂. Cilia beat frequency declined in excised lateral cilia (lc) exposed to increasing CO₂ levels, which appears to account for decreased clearance rates observed in field and laboratory experiments. Our data suggest that under conditions of increased CO₂ blue mussels will experience changes in physiological filtration, feeding rates, and cilia beat function that could have consequences for fitness and performance.