Luna had extensive experience with underwater archaeological sites in the Caribbean and the Gulf of Mexico, but Hoyo Negro presented challenges that exceeded almost any previous project in the field.

The basic rules of archaeological excavation apply even at the bottom of a flooded pit: document everything in place before anything is moved, record the spatial relationships between objects, sample systematically, disturb as little as possible.

Applying these rules at the bottom of Hoyo Negro required equipment and techniques that had to be developed specifically for the site.

The divers used modified photogrammetry systems — methods of making three-dimensional maps from photographs — to document the exact position of every bone and artifact before anything was touched.

They used specialized containers and collection methods to preserve water samples and organic material for dating and DNA analysis.