Geographic Information Systems (GIS) have revolutionized archaeological research by enabling precise spatial analysis, site mapping, and predictive modeling. This study examines the application of GIS at the Kymissala archaeological site on the island of Rhodes, Greece, where GIS technologies have been instrumental in uncovering settlement patterns, burial sites, and ancient trade networks. By integrating remote sensing and geospatial analysis, researchers have successfully identified previously unknown necropoleis and subsurface structures, reconstructed ancient road systems, and assessed environmental factors influencing settlement distribution. The study highlights GIS’s role in non-invasive archaeological research, cultural heritage preservation, and landscape reconstruction. Key findings indicate that settlements at Kymissala were strategically positioned near water sources and elevated terrains, reflecting defensive and economic considerations. Additionally, GIS has mapped trade routes connecting Kymissala to other Aegean centers, reinforcing its historical significance. Despite its advantages, GIS-based archaeology at Kymissala faces challenges such as data gaps, preservation threats, and the need for ground-truth verification. Future research should focus on AI-enhanced predictive modeling, advanced 3D site reconstructions, and enhanced remote sensing techniques to further archaeological knowledge while ensuring long-term site conservation. This case study underscores GIS’s transformative potential in archaeology, demonstrating how digital spatial technologies can expand historical understanding, optimize excavation strategies, and safeguard cultural heritage sites for future generations.