The urban heat island effect (UHI) is among the major challenges of urban climate, which is continuously intensifying its impact on urban life and functioning. Against the backdrop of increasingly prolonged heatwaves observed in recent years, practical questions about adaptation measures in cities are growing—questions that traditional meteorological monitoring can hardly answer adequately. On the other hand, UHI has long been the focus of research interest, but due to the technological complexity of providing accurate spatially referenced data at high spatial resolution and the requirement to survey at strictly defined parts of the day, information provision is becoming a major challenge. This is one of the main reasons why UHI research results are less often used directly in urban spatial planning. However, advances in geospatial technologies, including unmanned aerial systems (UASs), are providing more and more reliable tools that can be applied to achieve better and higher-quality information resources that adequately characterize the UHI phenomenon. This paper presents a developed and tested methodology for the rapid and efficient assessment and mapping of the effects of surface urban heat island (SUHI). It is entirely based on the integrated use of data from unmanned aerial systems (UAS)-based remote sensing methods, including thermal photogrammetry and GIS-based analysis methods. The study follows the understanding that correct SUHI research depends on a proper understanding of the urban geosystem, its spatial and structural heterogeneity, and its functional systems, which in turn can only be achieved by supporting the research process with accurate and reliable information resources. In this regard, the possibilities offered by the proposed methodological scheme for efficient geospatial registration of SUHI variations at the microscale, including the calculation of intra-urban SUHI intensity, are discussed in detail. The methodology builds on classical approaches for using local climate zoning (LCZ), adding capabilities for precise delineation of individual zone types and for geostatistical characterization of the urban surface heat island (SUHI). Finally, the proposed scheme is based on state-of-the-art technological tools that provide flexible and automated capabilities to investigate the phenomenon at microscales, including by enabling flexible observation of its dynamics in terms of heat wave manifestation and evolution. Results are presented from a series of sequential tests conducted on the largest residential area in Bulgaria’s capital city, Sofia, in terms of area and population, over a relatively long period from 2021 to 2024.