An osteometric–statistical study of residual rickets (RR) skeletal plasticity has been made of a time-ordered sequence of 11 series of adult skeleton sets (n=251) from shellmound sites around San Francisco Bay (the Bay) spanning the three archaeological horizons of Central California Indian prehistory in this region: Early (EH), Middle (MH) and Late (LH). To control for major differences of subsistence ecology and ethnolinguistic affiliation, the Bay sequence was further subdivided into four subregions: East (EB, Costanoan), South (SB, Costanoan, high acorns), West (WB, Costanoan, low acorns) and Northwest (NWB, Coast Miwok). In the eight EB series, a non-linear downward trend in cranioskeletal size was observed between EH and LH2, coinciding with a modest upward trend in the RR-15B score. To ascertain if food calcium deficit (CADEF) can explain the observed secular decline in cranioskeletal size, the evolving aboriginal Bay archaeodiet—relatively high in marine mammals, birds, fish and calcium-rich mollusks—was reconstructed by the diet grid method: in the three subregions with large stands of oaks (EB, SB, NWB), CADEF rose from negligible in the EH to moderate in the LH, as the subsistence base became more dependent on leached acorn meal for energy. Temporal and areal variation in Bay cranioskeletal size relates mostly to CADEF, demographic stress in females (DS), and the ‘male nutritional advantage interaction co-factor’ (MNAIC), in descending order of importance. This study has also confirmed the existence of the San Francisco Bay Indian physical type.