Dr. Beverly Goodman, with her then graduate student Rohi Jaijel (now Dr. Rohi Jaijel), undertook the marine geoarchaeology component of the project. This involved the collection of sediment cores around Vista Alegre in 2011 and then around the broader Yalahau/Holbox Lagoon in 2016. The cores were subjected to multi-proxy lab analyses (Loss on Ignition [LOI], δ18Ocarb and δ13Ccarb of bulk carbonate, grain size analysis, micropaleontology, and AMS radiocarbon dating). These analyses, in particular the micropaleontology work, revealed a much changed landscape around Vista Alegre over the past 3000 years. In the past Vista Alegre appears to have been positioned on a peninsula that jutted into the Yalahau lagoon. The mangroves and restricted shallow bays around the site seem to have formed over the last millennium and would not have been present when Vista Alegre functioned as a port site.
In addition, the coring campaign was augmented with a marine geophysical prospection program. This was done with a stratabox and revealed deeper basins in the east bay area around Vista Alegre. These basins are hidden by modern sediments but they could have cleared out in the past to make deeper harbor areas for the large canoes that would have been visiting the site.
