Groundwater level monitoring is crucial for assessing hydrological responses to climate change and human activities, which pose significant threats to the sustainability of semi-arid aquifers and the cultural heritage they sustain. This study presents an integrated remote sensing and transformer-based deep learning framework that combines diverse geospatial datasets to predict spatiotemporal variations across the plain near the Persepolis and Naqsh-e Rustam archaeological complexes-UNESCO World Heritage Sites situated at the plain's edge. We assemble 432 synthetic aperture radar (SAR) scenes (2015-2022) and derive vertical ground motion rates greater than -180 mm yr(-1), which are co-localized with multisource geoinformation, including hydrometeorological indices, biophysical parameters, and terrain attributes, to train transformer models with traditional deep learning methods. A sparse probabilistic transformer (ConvTransformer) trained on 95 gridded variables achieves an out-of-sample R-2 = 0.83 and RMSE = 6.15 m, outperforming bidirectional deep learning models by >40%. Scenario analysis indicates that, in the absence of intervention, subsidence may exceed 200 mm per year within a decade, threatening irreplaceable Achaemenid stone reliefs. Our results indicate that attention-based networks, when coupled to synergistic geodetic constraints, enable early-warning quantification of groundwater stress over heritage sites and provide a scalable template for sustainable aquifer governance worldwide.