Agricultural, industrial, and domestic activities are major contributors to the contamination of natural environments. The aim of this study is to assess the level of sediment contamination by organic pollutants in three Moroccan lagoons: Moulay Bousselham, Oualidia, and Khnifiss. samples were analyzed using liquid chromatography (LC) coupled with mass spectrometry (MS) in Multiple Reaction Monitoring (MRM) mode to detect organophosphorus, carbamate, urea and its derivatives, and other chemical groups. Gas chromatography (GC) coupled with mass spectrometry (MS) was also used to analyze organochlorines. The samples were subjected to dispersive solid-phase extraction (dSPE) using QuEChERS before analysis. Fifteen (15) active substances were detected, including organochlorines, organophosphates, carbamates, ureas, pyrethroids, and others. Three active substances, known for their high toxicity in aquatic environments (carbendazim, malathion, and chlorpyrifos), were identified. The heptachlor molecule (organochlorine family), although banned in Morocco, was still detected in the sediments of the lagoons of Oualidia and Khenifiss. Given the potential harm that these pesticides can cause to living organisms, it is crucial to introduce new crop protection techniques to address this issue.