In the Middle to Late Neolithic, pile-dwellings existed in Russia only in the Dnepr-Dvina basin and in the European region, in the Alpine zone, and probably in the western Baltic region. Investigations of sites in the Dnepr-Dvina region with underwater excavation methods have been conducted since the 1970s. The history of the development of these methods is presented here. The preliminary results of complex investigations of the Serteya II site are also covered in this article. An analysis of the remains of fauna, palynological analysis, and traceological analysis of bone tools, and modelling with GIS-technologies, allowed us to recreate the economic activities of the inhabitants of the Serteya II settlement. It had a complex character: it was a hunter-gatherer economy that existed alongside a small productive economy. The latter probably had a prestigious character, and did not play a significant role in the economy of ancient people. A comparison of data from typo-technological pottery inquiries with dendrochronological and radiocarbon dates allowed the determination of peculiarities of the material culture of every construction, and the distinguishing elements of local and newly arrived cultures. An analysis of types of wood allowed us to determine the areas of their origin, and to understand when and from what kind of forest repairs were made. Research shows that further investigation in this region will lead to uncovering other pile-dwellings.