This article deals with the economy-wide material flows in the Czech Republic in 1990–2006. It presents in brief the overall trends of the material flow indicators in 1990–2002. The major part of the article is focused on the years 2002–2006, which immediately preceded and followed the accession of the Czech Republic to the European Union in 2004. It is shown that this accession had quite a significant impact on the volume and character of the material flows of the Czech Republic. The accession was beneficial from an economic point of view, as it allowed for an increased supply of materials needed for economic growth. Furthermore, it was accompanied by an improvement in the efficiency of material transformation into economic output. From an environmental and broader sustainability point of view, however, this accession brought about some controversial outcomes. There was a significant increase in the net export of environmental pressure, on one hand, and an increase in net additions to the physical stock of the economy, on the other. Although the former is controversial from the viewpoint of equity in sharing area and resources, the latter places an additional burden on future generations because all physical stocks will turn into waste and emissions at some point, when their life span expires.