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A method of the Holocene paleoenvironment reconstruction based on the analysis of pedobiomarkers in tell deposits is suggested. On the Yunacite tell, such a reconstruction has been accomplished applying two types of environmental records: (a) soil records documented in the profiles of two soils within the middle and lower parts of the tell and reflecting changes in the conditions of pedogenesis averaged over relatively long periods and (b) soil-sedimentary records in the cultural deposits of the Eneolithic and the Early Bronze Ages (3.5 and 2.5 m in thickness, respectively). The lower soil identified at the depth of 9.2–10.0 m was buried about 5000 cal BC (the chronology is based on calibrated 14C dates). The low humus and high carbonate contents indicate arid climate conditions in the 6th millennium BC. The middle soil at a depth of 5 m was formed for about 1500 years (4350–2850 cal BC) according to 14C data. According to chemical and micromorphological analyses, it has a higher humus content and is more leached of CaCO3, as it was formed under more humid climate conditions. A detailed time record of CaCO3 leaching processes has been revealed in the sediments of the Eneolithic and the Bronze ages that were accumulating for about 600 years in the 5th millennium BC and for about 350 years in the 3rd millennium BC. Due to the increase in climate humidity, the leaching process was intensified twice: about 4500 and 2800 cal BC. In the same two periods, especially in the former period, the proportion of residues of hydrophilic beech increases significantly, and the proportion of oak residues decreases. Similar data have been obtained by the analysis of phytoliths and pollen.