Flint, or chert, sources in the Rhine-Meuse delta are generally distinguished based on macroscopic characteristics such as fossil inclusions, colour variations, and translucency. Previous studies on chemical characterisations of flint sources proved challenging due to the variation and overlap between different sources. Energy Dispersive X-ray Fluorescence (ED-XRF) analysis, therefore, cannot, in our view, be used as an alternative to these traditional sourcing methods. Nevertheless, in this paper, we demonstrate that X-ray spectrometry can be used as a viable method when used in tandem with traditional methodologies. Macroscopically, Spiennes and Lanaye flints, notably Rijckholt flint, cannot be distinguished based on variations in colour, texture, and microfossil content. In the present study, we used a non-destructive portable ED-XRF to distinguish Spiennes, Rijckholt, and eluvial Lanaye flints. While it proved impossible to distinguish between different Lanaye sources, it is possible to distinguish between Spiennes and Lanaye flints based on the higher phosphorus concentrations in Spiennes flint. The archaeological implications have been studied using material derived from four Neolithic Vlaardingen Culture (3400–2500 BC) sites in the Rhine-Meuse delta. We demonstrated that Spiennes and Lanaye flints were present at all sites. Proximity to either of these sources was not a decisive factor in procurement strategies. Flint was exchanged both via the Meuse (leading to the Lanaye flint sources) and the Scheldt (leading to Spiennes). The four selected Vlaardingen Culture sites are located at the intersection between these exchange routes. This favourable location provided good access to high-quality exotic flint at these sites.