In the side galleries of the former church, a permanent exhibition on Croatian underwater archaeology is presented, based on research conducted by ICUA Zadar. Through displayed archaeological exhibits, visitors can discover the richness of submerged heritage. The permanent exhibition is enhanced with virtual content, tactile screens, and VR glasses, offering an interactive and engaging insight into the fascinating world of underwater archaeology.

The ground floor of the former church is adapted for hosting temporary exhibitions but also serves as a multifunctional space for seminars, lectures, concerts, and other cultural and social events. A newly built Pavilion in the courtyard is used for educational and scientific demonstration workshops for all target groups, as well as for seminars, presentations, and interactive newly created content.

The reception building is designated for visitor reception, a souvenir shop, and a bookstore.

The entire space of the Educational and Presentation Centre for Underwater Archaeology St. Nicholas is adapted for people with disabilities.