The synergic effect between the spatial organisation and freight transport is crucial for transport planners to understand. It will help in improving freight transport planning. The absence of freight data has made such a study difficult. This research aims to understand the relation between spatial organisation and freight transportation by using the 1681 logistics facility database and the database of 2.65 million shipments of the Netherlands collected by CBS in 2015. The logistics facilities are categorised based on different spatial and logistics characteristics. The indicators of freight activity for the logistics facilities are studied, and the transport efficiencies are analysed subsequently. The analysis concluded on three main points. First, there are eight main types of logistics facilities in terms of spatial characteristics. Second, spatial characteristics have an impact on freight activity. Finally, the transport efficiency of the different logistics facilities can not be directly compared due to their objective and position in the supply chain.