We analyzed long-term and annual groundwater level fluctuations in the Kamennaya Steppe Nature Reserve in Voronezh Region based on monitoring data from the Dokuchaev pit. This pit is a unique groundwater monitoring site with the longest observation period in Russia and Europe, amounting to 130 years. The specific feature of groundwater formation of the Quaternary horizon, penetrated by the the pit, is that the annual and multi-year regime of groundwater levels is determined by the dynamics of infiltration water exchange between groundwater and the surface. The analysis is based on an extensive factual record, including a long-term series of hydrogeological observations and meteorological database. A set of methods and approaches was used: statistical methods, correlation analysis, SURFBAL water balance calculations, etc. Cross-correlation analysis of water levels in the pit and other observation wells on the Quaternary horizon revealed that the Dokuchaev pit is a representative observation point to assess the patterns of fluctuations in groundwater levels in the Kamennaya Steppe. Based on the analysis of time series it was found that the observed dynamics of water level in the pit follows the course of the main regime-forming factors, i.e., precipitation and potential evapotranspiration, determining the excess or deficit of water for infiltration in a multi-year framework. An extreme decrease of the water level in the pit to its partial drying in 2020–2022, as observed during the last 15 years, relates to dynamics of these factors. Based on model studies, it was shown that there is a gradual transformation of the annual regime of fluctuations of water level in the pit in the late 20th and early 21st century compared with the mid-20th century due to changes in conditions of spring–winter absorption of moisture from the surface of the earth and the formation of infiltration recharge. However, it is not as significant as, for example, the transformation of river hydrographs in the Don basin.