Traditionally the past has been investigated through the physical material remains. Specialists are now increasingly working within multidisciplinary frameworks to bring these specialisms together to construct broader narratives. While these material aspects form the majority of archaeological research topics, the associated intangible relationships, such as spatial context, are still poorly understood and have received limited investigation. This paper presents a series of case studies from the Dutch Late Neolithic wetlands to highlight various multi-disciplinary methodological issues which exist when applying spatial analysis to settlement remains. This is aimed particularly at the restrictions which can be faced, and potential solutions, when investigating the social use of space.