Using infrared thermography (IRT) has been proven as an effective technology for early damage detection within the superstructure/substructure of the ballasted railway tracks. Performing statistical processing and integrating principle component analysis (PCA) underpinned by extensive data sources of infrared imaging technology can effectively detect complex features exhibiting temperature variation. The present study employs these processing techniques on thermal images to investigate the drainage health of railway ballast layer using IRT technology. Specifically, clean and clay-fouled ballast specimens are prepared to study the effect of contamination/fouling in ballast layer (porous granular media) on water retention (indicated by water level) during severe rainfall intensity. IRT is utilized to monitor the water level as the indicator of ballast layer drainage health condition. Results show that the IRT image-processing technology confirms the capability of IRT for detecting water surface/water retention based on the thermal images captured from ballast specimen surface. In addition, an appropriate time for monitoring via IRT is after heavy rainfall upon which the water retention in the ballast layer can be more effectively detected. Particularly, presence of water and fouling material among ballast particles results in lower and more uniform surface temperature compared to dry or clean ballast specimens.