The Opalinus Clay is an argillaceous to silty mudstone formation, notable in Switzerland as the selected host rock for deep geological disposal of radioactive waste. Its upper bounding unit (Passwang Formation and eastern equivalents) is composed of successions of mudstone, sandy bioclastic marl and limestone separated by ooidal ironstone beds. The lithostratigraphic transition is diachronous across northern Switzerland and shows high vertical and lateral lithological variability. To constrain this variability into predictive models, and to identify horizons with properties that could potentially influence radionuclide mobility, the sedimentological and diagenetic processes involved in the genesis of this transition have to be investigated. The present study aims at testing the applicability of X‐ray fluorescence chemostratigraphy to characterise the mixed carbonate–siliciclastic units and understand the complex genesis of the lithostratigraphic transition from the Opalinus Clay towards its upper bounding unit. Sediment drill cores from four locations across northern Switzerland (Mont Terri, Riniken, Weiach and Benken) are analysed using high‐resolution X‐ray fluorescence core scanning. Data are compared to petrographic and additional geochemical data sets (inductively coupled plasma mass spectrometry, scanning electron microscopy with energy dispersive X‐ray analysis, micro‐X‐ray fluorescence mapping) obtained from powdered samples, thin section analyses and drill core slabs. The results demonstrate that the combination of these rapid and non‐destructive measurements along with multivariate data analysis allows the fast and objective classification of lithofacies along complex sedimentary successions. Moreover, it provides quantitative means for differentiating between prominent depositional and post‐depositional processes. The lithostratigraphic transition has been traced by the use of specific elemental proxies as a discontinuity, and its genesis linked to sediment bypassing.