Every year a variety of vector-borne infectious diseases claims the lives of millions of people worldwide. The study of the favorable conditions for their vectors and hosts is a particularly important task for understanding the patterns of the distribution with the focus on the urban environment, characterizing by a high population density and rapid transmission of the diseases. The existing methodology of Local Climate Zones (LCZ), which are areas with homogeneous land surface coverage, structure, and a specific nature of human activity was the first attempt to standardize urban environmental studies and has become an international standard for the analysis of urban morphology. The article provides an algorithm for adapting the methodology of identifying LCZ accounting vegetation and water areas for the tasks of medical geographical zoning and assessment of epidemiological risks and using the geographic information technology. The examples of the outbreaks of vivax malaria in the Moscow region in 1999–2003 and West Nile fever in the Volgograd region in 2010–2011 were used. As a result, a methodology of medical geographical zoning based on the idea of fragmenting the classification of LCZ using the normalized difference water index as indicator of the favorability for vector habitats was developed. The use of the methodology made it possible to reveal that the areas of various LCZs change after outbreaks, which may reflect changes in conditions and an increase in the favorability for vectors. Thus, LCZ can be used as indicators of changes in the natural and man-made environment that can provoke disease outbreaks.