There are multiple challenges in analysing pigments in historic watercolour paintings on paper, and typically non-invasive, in situ methods are required. Recent developments in portable analytical instrumentation have made this more accessible to heritage institutions, but many commercial systems are not optimised for the specific requirements of manuscripts and works on paper. This paper describes the successful use of Raman spectroscopy, X-ray fluorescence spectroscopy (XRF) and hyperspectral imaging to identify and map watercolour pigments used by the eighteenth century botanical illustrator, Ferdinand Bauer, and demystify the unusual colour code system found in his sketches. The value, delicate nature and large size of these paintings necessitated the use of using in situ, non-contact methods of analysis. A portable, bespoke Raman spectrometer specifically designed for analysing pigments from works on paper was used together with a bespoke portable Fibre optic reflectance spectrometer, portable X-Ray Fluorescence spectrometer and a hyperspectral imaging sensor. The results demonstrate that although there is a significant compromise between achieving good Raman spectroscopic results from artists’ pigments and using sufficiently low laser power densities so as not to cause damage to the pigments, good results could be obtained with this portable system, particularly when combined with XRF, fibre optic reflectance spectroscopy (FORS) and hyperspectral imaging. Eight pigments were identified unequivocally from 125 watercolour paintings analysed, suggesting that Bauer used a more traditional and more limited palette than previously considered, and that his palette changed significantly in his later paintings. Similar pigments identified by the authors on colour chart that was discovered in 1999 in Madrid and attributed to Bauer, add weight to the attribution of this chart to Bauer. The data provides a much deeper insight into Bauer’s colour annotations, and how he was able to achieve such an impressive degree of colour fidelity in his work.