The lakeshores of western Switzerland are one of Europe's best-known Neolithic settlement areas, thanks to dendrochronological dating and the exceptional preservation of organic materials. Against this outstanding background, this study uses zooarchaeological data to answer a series of questions regarding the Neolithic economy, environment and human-environment interactions at these lakeshore sites. It also discusses, within an interdisciplinary framework, the possible impact climatic fluctuations, cultural influence, topographical conditions, and demographic growth had on economic change. The results show that the faunal economy was mainly based on animal husbandry, with fluctuations in the cattle-pig ratio. Hunting also played an important role in the food system and focused mainly on large game, especially red deer, which contributed significantly to the meat supply. The results from comparing these animal bone remains also show that multiple factors, such as topography, climatic conditions, and cultural influence, played a part in the socio-economic organisation of the Neolithic communities. Exploratory procedures such as correspondence analysis support these interpretations.