This data set include geochemical, color and magnetic susceptibility data from the alpine wetland of Laguna Seca in the southern Iberian Peninsula. These data cover the last 15.8 kyr and were used to reconstruct the paleoenvironmental evolution of this alpine lake since the last deglaciation. These paleoenvironmental data were obtained from a sediment core, LS-01, which was retrieved in 2014 with a Rolatec RL-48-L drilling machine equipped with a percussion corer. Magnetic susceptibility was measured at the Department of Stratigraphy and Paleontology of the University of Granada using a Bartington MS2E meter in the International System of Units (SI × 10^(−6) at 0.5 cm intervals over a period of 20 seconds. Bulk organic geochemical data (total organic carbon (TOC) and total nitrogen (TN)) were measured using a Thermo Scientific Flash 2000 CHNS Elemental Analyzer at the Centro de Instrumentación Científica of the Univeristy of Granada after sample digestion with HCl 1N. TOC and TN data are expressed as percentages. Inorganic geochemical data (Al, Si, Fe, K, S, Ca, Rb, Zr, and Br) were measured using an X-ray fluorescence (XRF) Avaatech XRF core scanner at the CORELAB laboratory of the University of Barcelona. Light elements were measured using a 700 μA X-ray current and a 10 kV X-ray voltage during a 10-second count time. For heavy elements, an X-ray current of 1300 μA and an X-ray voltage of 30 kV were used for 35 seconds. Results are expressed in counts per second (CPS). The color spectra of the LS-01 core were obtained at 0.73-mm intervals with an f/6.7 aperture and a 5-second exposure time using the Avaatech XRF core scanner camera at the CORELAB laboratory of the University of Barcelona. These data were resampled to fit the sampling resolution of the MS and the XRF core scanner measurements.