This dataset complies carbon and nitrogen isotopic and elemental signature for two dated lacustrine sediment core for the Khnifiss Lagoon, Southern Morocco, for the last century. Chronological data retrieved from 210Pb and 137Cs measurements are also available for these cores. We have also analysed local vegetation specimens, based on the vegetation list of the Khnifiss National Park for their elemental and isotopic analysis of C and N. The cores measuring approximately 50 cm were collected manually from a boat employing a gravity core sampler. The cores were sliced every two centimeters in the field, packed in individual identified plastics bags, and kept refrigerated. The sedimentation rates and chronology of each sediment layer were determined by the CRS (Constant Rate of Supply) model (Appleby & Oldfield, 1978) using natural radionuclides 210Pb and 226Ra and the 1965 bomb peak for 137Cs. The sediment samples were dried in an oven at 50°C for 48 hours, ground in an agate mortar, and stored in sealed disposable plastic Petri dishes. The samples were weighed, and the densities were measured. The high-resolution gamma-ray measurements were performed for 24 hours for each sample using a plane co-axial extended range germanium hyper pure detector (model GX5021 - Canberra), installed at the Department of Physiological Sciences of the Espírito Santo Federal University (UFES), Brazil. Detector relative efficiency is 50%, with a resolution of 2.1 KeV (FWHM) at the 60Co peak (1.33 MeV). Efficiency curves for sample geometry were obtained from a liquid solution containing a mixture of radionuclides (NIST - serial number HV951), including 133Ba, 57Co, 139Ce, 85Sr, 137Cs, 54Mn, 88Y, and 65Zn. Total carbon, nitrogen, and sulfur elemental concentrations were determined with an elemental analyzer Vario El III Elementary (Elementar). Before the δ 13C and Corg determination, an aliquot of the crushed samples was subjected to acid attack (HCl 3%) until the carbonate fraction was removed. Nitrogen and carbon isotopes were analyzed with a FlashHT 2000 elemental analyzer coupled with a Delta V Advantage mass spectrometer from Thermo Fisher Scientific. The δ13C is expressed in per mil (‰) against the international standard VPDB (Vienna Pee Dee Belemnite), and the δ15N in per mil (‰) against Air. The Khnifiss National Park vegetation samples, composed of twigs and leaves, were packed in individual plastic packages and identified to species level, when possible, and later dried in a 50°C oven for 48 hours and ground in an agate mortar at the Faculty of Science, Ibn Zohr University (Agadir, Morocco). Finally, the samples were sent for elemental and isotopic analysis of C and N in the Thermo Fisher Scientific FlashHT elemental analyzer coupled to the Thermo Fisher Scientific Delta V Advantage mass spectrometer. The samples for particle size analysis were treated with 1 N HCl at 25 °C to remove carbonates. Once the digestion process is completed, the samples were washed with distilled water and then were centrifuged at 4000 rpm, after which the supernatant was carefully removed using a Pasteur pipette. After this step, the samples had their organic matter content removed by treatment with concentrated hydrogen peroxide (30%) that was continually added to the sample in a hot plate at 60°C until sample frothing ceased. Thus, only the mineral fraction of the sample remained, presenting no agglutination between the particles. Into this content is was added a dispersant, sodium hexametaphosphate ((NaPO3)6, in the concentration of 40mg/L), thus avoiding the aggregation of particles, which could interfere in the determination of the particles size distribution. The samples were shaken for 24 hours and then analyzed in the CILAS® 1064 Particle Analyzer. The CILAS 1064 has a dual sequenced laser system for a measuring range of 0.04 to 500 µm and delivering the results in 100 interval classes. For the determination of chlorophyll derivatives in sediment, we applied the method described by Sanger et al. (1972). The “sedimentary chlorophyll”, a product of chlorophyll degradation, was extracted from sediments by placing approximately 1g of wet sample to a centrifuge tube, protected from ambient light with laminated paper and by adding 20 mL of 90% acetone in each tube. The tubes were left on a shaking table, in a semi-dark environment, for approximately 20 minutes for two consecutive times, interspersed by centrifugation and removal of the supernatant, and with a third extraction, adding 10 mL of acetone. The absorbance of the extract was measured in a scanning spectrophotometer with a range of 350 to 800 nm. The possible interferences in the absorbance background were corrected by subtracting the chlorophyll peaks from a baseline curve made between 500 nm and 800 nm, thus eliminating the absorbance of non-chlorophyll components (Wetzel, 2001). The concentrations of pigments are expressed as the Sediment Pigment Derivative Unit (SPDU) per gram of organic matter (Vallentyne, 1955). Finally, the concentrations of Sr, Ca, Si e Ti were determined using an Epsilon 3X energy dispersive X-ray fluorescence (EDXRF) spectrometer, PANalytical. A total of 50 samples (26 and 24 for THI and THIII, respectively) were milled into powder and transferred to an open-ended XRF cup covered with 3.6 µm PANalytical thin-film. The reference concentration for each element was based on the concentration of the element, using inter-element slope and baseline-corrected peak heights from the XRF system.