Honen Dalim was built from yellow brick made in Holland that was imported as ballast to Statia. In the early 1980's archaeologist Dr. Norman Barka from the College of William and Mary began excavations inside Honen Dalim. He found evidence for many architectural elements pointing to the interior layout of the building. Joist holes were identified for supporting a wooden floor. In the center of the building, brick footers were found that are the remains of the Bimah (among Sephardic Jews, the Tebah) where the Torah was read. The exterior brick stairs leading the women's gallery are still standing as are the joist holes that once held beams supporting the gallery. At the eastern end of the synagogue was evidence for the Aron Kodesh (among the Sephardim, the Heikhal) where the Torah Scrolls were kept. The William and Mary team found no artifacts related to Judaism.

In 2005 the Sint Eustatius Center for Achaeological Research headed by Grant Gilmore PhD made a huge discovery. While attempting to locate a tunnel that was supposed to have been used to store the Torah, Menorah and other valuables, his team excavated the actual Mikveh for Honen Dalim. It was beautifully built of cut stone with a white plastered intererior with steps leading the bathers to an immersion depth of just under 2 meters in the bath. The Mikveh at Honen Dalim was only the second to be excavated anywhere in the Americas. Dr. Gilmore is credited with this excavation of great significance and is very knowledgable and supportive of this restoration project.