AbstractNatural organic matter (NOM) is a key parameter in aquatic biogeochemical processes. Part of the NOM pool exhibits optical properties, namely absorption and fluorescence. The latter is frequently utilized in laboratory measurements of its dissolved fraction (fluorescent dissolved organic matter, FDOM) through excitation–emission matrix spectroscopy (EEMS). We present the design and field application of a novel EEMS sensor system applicable in situ, the ‘Kallemeter’. Observations are based on a field campaign, starting in Norwegian coastal waters entering the Trondheimsfjord. Comparison against the bulk fluorescence of two commercial FDOM sensors exhibited a good correspondence of the different methods and the ability to resolve gradients and dynamics along the transect. Complementary laboratory EEM spectra measurements of surface water samples and their subsequent PARAFAC analysis revealed three dominant components while the ‘Kallemeter’ EEMS sensor system was able to produce reasonable EEM spectra in high DOM concentrated water bodies, yet high noise levels must be addressed in order to provide comparable PARAFAC components. Achievements and limitations of this proof-of-concept are discussed providing guidance towards full in situ EEMS measurements to resolve rapid changes and processes in natural waters based on the assessment of spectral properties. Their combination with multiwavelength FDOM sensors onboard autonomous platforms will enhance our capacities in observing biogeochemical processes in the marine environment in spatiotemporal and spectral dimensions.