Occupying 4% of Crimea’s territory, the sub-Mediterranean landscapes of Southern Crimea stand out for their distinct soil-climatic conditions and record of human activity. This paper presents the results of study of the newly formed and well-dated soils from 21 archaeological sites, making it possible to build a soil chronosequence covering the last 2.3 ka. To study the natural processes on an intra-secular scale, short series of instrumental meteorological observations were extended, based on dendrochronological records, to a total of 160 years, and the time series of solar activity and energy for pedogenesis were correlated. These data are collated with a 4.2-ka Lake Saki varve record, which was re-analysed applying the DFT spectrum analysis method, with three distinct phases in relative secular variations in precipitation being identified. The phase of a relative climatic stability with moderate variations in precipitation (3.2–1.25 ka BP) was followed by the period of increased moisture (from 1.25 ka BP), unparalleled since the Late Bronze Age. Given the decisive role of increased moisture in the climate-controlled energy expenditures for pedogenesis, in the dynamics of vegetation cover and human ways of life, the identification of these periods contributes to a better understanding of soil–climate relationship and cause-and-effect for nonlinear change in the settlement and landscape history of the region.