The settlements of the Linear Pottery Culture (LBK) have been a major topic of research on the Early Neolithic (5500-4900 BC) in Central Europe for almost a century. However, despite many years of research, we are still unable to fully answer the fundamental questions of how these settlements were formed, which limits any research focused on, for example, chronology or socio-economics. Therefore, the study of taphonomy and waste management is in this context crucial. This paper presents a case study focusing on waste management at the LBK settlement in Hlízov (Czech Republic). The study analysed the fragmentation, refitting, and concentration of artifacts in the pits surrounding house-ground plans. The results indicate that waste management was much more complex than previously thought. It was found that each type of waste (pottery, chipped stone, ground stone) seems to be treated differently by Neolithic people. The case study shows that without waste management and taphonomy research, our understanding of everyday life at the settlements could be misleading and over-optimistic. The examined finds provide authentic testimony of human behavior in relation to waste management in the settlement space that constitutes a prerequisite before dealing with more complex issues like socio-economics, households or identity of the Neolithic communities.