This study integrates several lines of evidence to assess temporal trends in the persistence of indigenous village communities in the San Francisco Bay-Delta area after the arrival of the Spanish in 1776 C.E. Baptismal records indicate that more than half of the Native American village communities in the region persisted as independent entities for at least another 25 years or longer. Archaeological evidence and radiocarbon and obsidian hydration results from post-contact native settlements are spatially patterned in a manner consistent with the archival record. Material indicators of the Mission Period (such as European material culture and non-native plant and animal resources) are also present at many radiocarbon-dated post-contact native settlements, indicating at least a limited movement of goods but also highlighting how these data sets are poor indicators of indigenous persistence during the early colonial era. The results provide a foundation for future research into initial reactions to the colonial intrusion from the perspective of traditional native communities.