The behavior of single layer van der Waals (vdW) materials is profoundly influenced by the immediate atomic environment at their surface, a prime example being the myriad of emergent properties in artificial heterostructures. Equally significant are adsorbates deposited onto their surface from ambient. While vdW interfaces are well understood, our knowledge regarding the atmospheric contamination is severely limited, even after the last decades of intense research in the field. Here we show that the common ambient contamination on the surface of: graphene, graphite, hBN and MoS2 is composed of a self-organized molecular layer, which forms during a few days of ambient exposure. Using low-temperature STM measurements we image the atomic structure of this adlayer and in combination with infrared spectroscopy identify the contaminant molecules as normal alkanes with lengths of 20–26 carbon atoms. Through its ability to self-organize, the alkane layer displaces the manifold other airborne contaminant species, capping the surface of vdW materials and possibly dominating their interaction with the environment.