Disease, overharvesting, and pollution have impaired the role of bivalves on coastal ecosystems, some to the point of functional extinction. An underappreciated function of many bivalves in these systems is shell formation. The ecological significance of bivalve shell has been recognized; geochemical effects are now more clearly being understood. A positive feedback exists between shell aggregations and healthy bivalve populations in temperate estuaries, thus linking population dynamics to shell budgets and alkalinity cycling. On oyster reefs a balanced shell budget requires healthy long-lived bivalves to maximize shell input per mortality event thereby countering shell loss. Active and dense populations of filter-feeding bivalves couple production of organic rich waste with precipitation of calcium carbonate minerals, creating conditions favorable for alkalinity regeneration. Although the dynamics of these processes are not well described, the balance between shell burial and metabolic acid production seems the key to the extent of alkalinity production versus carbon burial as shell. An estimated alkalinity budget is presented that highlights the significant role oyster reefs once placed in the Chesapeake Bay inorganic carbon cycle. Sustainable coastal and estuarine bivalve populations require a comprehensive understanding of shell budgets and feedbacks among population dynamics, agents of shell destruction, and anthropogenic impacts on coastal carbonate chemistry.