The historic and architecturally significant buildings and structures that comprise the coastal fortifications around San Francisco Bay have suffered extensive past deterioration and continue to suffer from the effects of active deterioration. Historic engineering records, in the form of annual reports from the Secretary of War, reported deterioration even as the batteries were under construction. Original architectural and engineering drawings for a number of the batteries were marked with specific recommendations for maintenance. Despite the effects of nature, historic use, and abandonment, the batteries and supporting facilities retain significant integrity of materials, context, and association. The consistency of the materials and construction techniques within each period leads to a certain consistency in the elements of deterioration.
Earthworks are in generally good condition with isolated erosion and soil instability.
Seismic activity and erosion have undermined some smaller concrete structures at Battery Townsley and Battery Crosby. Battery Mendell was placed on an eroding sand hillside and has developed serious structural problems. Other batteries including Battery Boutelle exhibit major cracking. Trails often contribute to erosion. At most batteries, soil migration and washing have affected surface drainage by obstructing positive drainage away from structures and filling surface and subsurface drainage systems.