Relevance. The conditions of complex structural and tectonic setting, insufficiency and uneven geological and hydrogeological exploration of mineral deposits in Eastern Siberia determine the relevance of the issues of optimization of hydrogeological works and reduction of their implementation costs. Aim. Identification of a number of readily defined, indirect indicators that predetermine the selection of sites promising for drilling hydrogeological wells. Methods. The two-stage method of system-model analysis was used to improve the efficiency of the project work. The first stage is training. It involves the use of the principal component analysis and ends with the compilation of a classification table of standard objects (thoroughly studied in geological and hydrogeological terms) in accordance with the earlier identified most significant indirect indicators but easily accessible ones. The second stage is recognition or forecast. It includes attribution of analogous objects (with poorly or unstudied geological and hydrogeological conditions) to certain classes determined at the first stage. When solving this problem, the programs implementing cluster and multiple regression analyses are used. As a result, the analogous objects are classified in accordance with the task set. Results. The developed methodology is used for various purposes: for structural hydrogeological zoning of the Ilim-Lena plateau with associated main iron ore deposits of Eastern Siberia, for typification of alluvial deposits of the Lena gold ore region according to the complexity degree of engineering hydrogeological conditions, for identification of sites featuring increased water abundance in the fields of the oil and gas complex of Eastern Siberia. The results obtained make it possible to recommend the method to be widely introduced into the practice of hydrogeological research. It is necessary for optimizing the types and volumes of special works at mineral deposits in order to identify the most water-abundant zones when developing dewatering and water supply systems under different-scale structural hydrogeological zoning. In addition, the method of system-model analysis provisioned with additional processing methods has a potential and is already widely used when dealing with databases and object typification according to environmental and hydrogeological indicators.