The paleogeographic study of one of the large Medieval settlements of the Jin Empire (1115–1234) in the Primorye was carried out in order to analyze the minor climatic rhythm during the settlement of a large river valley. New data on the chronology of the settlement were obtained using radiocarbon dating of charcoal and tephrostratigraphy. It was established that the territory began to be developed by the Krounovskaya culture (4th century BC to the 3rd century AD) under relatively dry conditions associated with a decrease in the summer monsoon intensity. In the 10th century the humidity increased sharply. The peak of warming occurred in the 11th century. At this time Medieval settlement appeared here, that existed before the construction of the fortress. The layers of this settlement lie under the ramparts. The study of pollen and diatoms in the cultural layers has allowed us to determine the characteristics of the environment during the Jurchen period (12th–13th centuries). Radiocarbon dating of the humus shows that the cultural layers contain redeposited organogenic material, which provides information on the pre-Jurchen environment. It has been established that significant changes in the natural steppe landscapes occurred in the early Middle Ages. Pollen data show signs of agriculture and other economic activities, including the plants’ cultivation, the development of ruderal plants and apophytes, as well as spores of pathogenic fungi. During the development of the territory in the Middle Ages, the main risks were associated with severe floods. Layers of loams found among the cultural layers indicate the repeated flooding of the fortress. Bioindicators of severe floods are allochthonous diatoms, represented by species that lived in the aquatic environment.