The paper presents the results of a palaeoecological study of Neolithic archaeological layers from a wetland, multilayer site, Serteya II (Western Russia). It contains, domestic structures, rich organic artefacts, skeletons, and ecofacts preserved within lacustrine deposits that are extremely important on a European scale. We employed a set of specialised palaeoecological analyses and accelerator mass spectrometry radiocarbon dating to identify the principal environmental conditions which attracted Neolithic hunter-fisher-gatherer communities from 4300 to 1600 cal. BC. The distinct impact of communities using a nonproductive economy on the ecology of the palaeolake shore zone was recorded. Also, palaeolake water level changes influenced the palaeoeconomic activity of local Neolithic societies, such as gathering of plants (for the medicinal use or serving as dietary components), fishing activities, and possible funeral practices. In addition, the identified phases of high-water level changes, which were responses to climatic oscillations, were correlated with supraregional climatic events, especially ca. 6.2, 5.9, and 4.2 ka cal. BP. Thus, our results allowed for the reconstruction of environment transformations and conditions of Neolithic communities' activity, as well as for a better understanding of the relationships between local Neolithic communities' way of life and neolithisation processes in Eastern Europe.