Modern strategies for preserving archaeological heritage increasingly employ digital technologies to document, analyze, and visualize sites that are either threatened with destruction or already lost. This article explores the integration of Geographic Information Systems (GIS) and three-dimensional (3D) reconstruction methods as a robust framework for conserving cultural heritage sites. Drawing on case studies – including the Maklasheevka IV burial ground, the Bish-Balta necropolis, the architectural ensemble of the Kazan Kremlin and the Lyashevo hillfort – this study demonstrates the potential of developing digital models across multiple scales, ranging from broad landscape reconstructions to high-resolution models of individual artifacts and architectural fragments. Particular emphasis is placed on the methodology for processing heterogeneous source data, which includes field surveys, archival materials, aerial imagery, and laser scanning data. The study examines international experience in the reconstruction of lost architectural ensembles in Central Asia, which is of special interest when dealing with fragmentary and incomplete sources. The integrated use of spatial analysis and 3D modeling makes it possible not only to create accurate virtual reconstructions but also to conduct detailed analyses, identifying missing elements and the structural features of the sites. The findings prove the efficacy of digital technologies for monitoring the condition of heritage sites, their scientific restoration and promotion.The proposed methodologies can be adapted to study various types of archaeological sites, thereby facilitating their preservation and comprehensive investigation.