Obsidian artifacts recovered from Mission Santa Clara in central California (1780s–1840s) provide the opportunity to evaluate the persistence of regional economic connections and stone tool technologies in the California missions. Portable x-ray fluorescence (pXRF) analysis was conducted on a sample of 1020 obsidian artifacts, which could be linked to five major geological sources of obsidian found in different regions of California. Obsidian source profiles from features in different areas of the site indicate differential access to or preference for obsidian from particular sources. Despite the small size of many of the obsidian artifacts in the sample, this study found that the use of pXRF was suitable for assigning small artifacts (> 0.3 cm) to regional obsidian sources. The results illuminate the connections that native people living in mission contexts may have maintained to outside resources and provide the basis for further investigation into indigenous stone tool traditions in colonial contexts.