Arunachal Pradesh, previously referred to as the North East Frontier Agency (NEFA), is a northeastern Indian state possessing a profound historical and archaeological legacy. Esteemed for its varied ethnic populations and distinctive geography, it encompasses significant locations like the archaeological site at Malinithan, established in the 13th–14th centuries CE. This location showcases a mediaeval temple adorned with sculptures of deities like Indra and Ganesh and is harmoniously situated within the local topography, particularly its closeness to the Brahmaputra plains and other waterways. Geographic Information Systems (GIS) enable the investigation of site distribution and environmental contexts, emphasising the impacts of terrain and resources on ancient communities. The research highlights the significance of GIS in archaeological methodologies, underscoring its contribution to heritage preservation and planning, along with its capacity to clarify the cultural landscapes of Arunachal Pradesh.