We investigate the potential of hyperspectral imaging spectrometry for the analysis of fresh sediment cores. A sediment-core-scanning system equipped with a camera working in the visual to near-infrared range (400 to 1000 nm) is described and a general methodology for processing and calibrating spectral data from sediments is proposed. We present an application from organic sediments of Lake Jaczno, a freshwater lake with biochemical varves in northern Poland. The sedimentary pigment bacteriopheophytin (BPhe ) is diagnostic for anoxia in lakes and, therefore, an important ecological indicator. Calibration of the spectral data (BPhe absorption to 900 nm) to absolute BPhe concentrations, as measured by high-performance-liquid-chromatography, reveals that sedimentary BPhe concentrations can be estimated from spectral data with a model uncertainty of . Based on this calibration model, we use the hyperspectral data from the sediment core to produce high-resolution intensity maps and time series of relative BPhe concentrations ( to 20 data points per year, pixel resolution ). We conclude that hyperspectral imaging is a very cost- and time-efficient method for the analysis of lake sediments and provides insight into the spatiotemporal structures of biogeochemical species at a degree of detail that is not possible with wet chemical analyses.