This data set comprises elemental data obtained from 101 sediment samples. The sediments originate from lakes in the Windmill Islands and a wide range of other lacustrine and marine settings and were selected to fingerprint the depositional environment (marine or lacustrine) based on the elemental composition. Geochemical analyses were performed on freeze-dried and ground material. Total organic carbon (TOC) and total inorganic carbon (TIC) were analyzed with a DIMATOC 200 analyzer (DIMATEC Corp.). Nitrogen (N wt%) and sulphur (S wt%) were measured with a Vario Mircrocube (Elementar). Inorganic elemental composition reported here was analysed with an ITRAX µXRF core scanner (Cox Analytical Systems, Sweden) with a Cr X-ray tube (settings: 30 kV, 55 mA). To convert the semi-quantitative XRF counts obtained with the ITRAX core scanner to absolute elemental concentrations, reference samples with known elemental compositions were analyzed along with each batch of samples and absolute element concentrations were calculated based on linear calibration curves for elements with a Pearson correlation coefficient R² >0.65. This data set was evaluated with principal component analysis (PCA) that was performed on standardized values with the programme past 4.04 as discussed in Small et al. (20xx). The data set is a supplement to the manuscript "Rapid relative sea-level fall during the mid-Holocene in the Windmill Islands, East Antarctica" submitted for publication in the journal Quaternary Science Reviews by Small et al. 20xx.