This dataset provides geochemistry data for the Holocene sediment sequence retrieved from Lake Uddelermeer (The Netherlands) in 2012. Concentrations of sedimentary pigments, fossil sterols and stanols as well as elemental (C, N) measurements are presented against both depth (cm) and age (cal yr. BP). A total of 92 samples were analysed for C, N and sedimentary pigment content; a subset of 30 samples was analysed for sterol and stanol compounds. The data provides an insight in the natural variability of the lake ecosystem and has been used to identify the anthropogenic drivers of the change to the turbid conditions that currently characterize this lake. Cores were retrieved from the centre of the lake using a 3-m long handheld piston corer deployed from a floating coring platform during field work in April and May 2012. Samples were obtained from splits of the core and processed in the laboratory of the University of Amsterdam (the Netherlands) using standard protocols, including the use of high performance ...