During a survey at southeast Morocco in 2017, a sediment core was manually extracted from the most continental part of the Khnifiss coastal lagoon, in the Saharan domain. The 227 cm sediment core was sliced into 1-cm layers. In 2018, the downmost 72 cm of these samples were dated and analyzed in 2-cm intervals for stable carbon isotope ratio (δ13C), total content of organic carbon and nitrogen, grain-size and elemental composition. The data collected covered a period of 3428 ± 29 cal yrs BP and was used to reconstruct the environmental changes occurred in the lagoon and to investigate their correlation with climatic changes occurred in the North Atlantic Ocean sector.