Fracture filling minerals and the smectite-group clay minerals in particular play a significant role in the geotechnical stability of the fractured rock mass. Smectites have multiple uses as geomaterials in waste management solutions, of which the most technically demanding is the geological disposal of radioactive waste. Here, the stability and occurrence of smectites as fracture filling minerals were studied with two main objectives: 1) to test the capability of short-wave infrared spectroscopy as a tool to streamline the site assessment where clay mineralogy needs to be characterised in detail, and 2) to provide a first assessment of naturally occurring smectites in various sample types collected from two Finnish sites (Olkiluoto and Hyrkkölä) and their potential as natural analogues of smectite stability for bentonite used in the engineered barrier systems of geological disposal repositories. The short-wave infrared (SWIR) method has been validated to be a useful tool in fracture mineral characterisation, specifically due to its fast acquisition and interpretation time compared to the conventional methods. The study confirms the in situ occurrence of smectites at both sites studied showing that, especially in Hyrkkölä, the smectite-group member is close to montmorillonite, the main constituent of bentonite. At Olkiluoto, the smectites studied show more interstratified features. The differences in the mode of occurrence are related to the history of their formation, especially hydrothermal alteration, and parent rock composition.