Many marine bivalves are sensitive to ocean acidification (OA) stress and often show heightened sensitivity during brief early larval and post-larval life stages, potentially leading to population bottlenecks. Most of the evidence to date has been collected in laboratory experiments that focused on physiological responses at the organismal level under stable carbonate chemistry. Bivalves, however, inhabit coastal and estuarine environments where multiple physical and biological processes affect carbonate chemistry and often result in significant temporal and spatial variability and decoupling of carbonate chemistry variables. Furthermore, bivalves often form large shell aggregations where biogeochemical feedbacks relating to inorganic C cycling and alkalinity have not been well constrained and, thus, aggregation-level responses to OA are largely unknown. This dissertation focuses on bivalve responses to OA on two biological organizational levels -organism and habitat- by 1) providing new frameworks to evaluate environmental variability and 2) measuring the potential of local OA buffering within shell aggregations. These two overarching goals should provide more realistic forecasts of the fate of bivalves under future climate scenarios. Chapter 2 describes a new metric to predict survival of Pacific oyster larvae by integrating their exposure history to variable acidification conditions. Chapter 3 presents a new experimental system capable of decoupling carbonate chemistry parameters and recreate variable exposures under a controlled laboratory environment. Chapter 4 provides the first measurements of alkalinity fluxes in oyster reefs, a type of bivalve aggregation, and evaluates the response of the system to moderate acidification conditions to evaluate the potential of shell aggregations to modify local carbonate chemistry conditions and provide buffering to OA for juveniles. Chapter 5 offers a detailed characterization of the biogeochemistry of a restored oyster reef and the identification of key biogeochemical processes responsible for alkalinity production or regeneration within porewaters. This dissertation suggests that relatively simple modeling and laboratory tools can successfully incorporate temporal variability naturally experienced by bivalves and provide adequate predictions of survival. It further provides first evidence that reef-level biogeochemical feedbacks derived from the collocation of calcium carbonate shell and labile organic matter result in the production of large alkalinity fluxes that, while not very sensitive to increased moderate PCO2, could indeed buffer corrosive conditions at local spatial scales, providing micro-refugia to sensitive larval and juveniles. Collectively, this body of work is proof of the need to shift from an OA open-ocean paradigm based on stable carbonate chemistry conditions to improve our understanding regarding OA impacts on sensitive coastal organisms exposed to dynamic carbonate chemistry conditions.