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As part of the routine control of the Tunisian network for the monitoring of the most problematic microalgae species Karenia selliformisand Alexandrium minutumand for the study of hydrophilic and lipophilic marine biotoxin profiles, clams and seawater samples from Boughrara lagoon were analysed during the past decade. The results showed that the abundance of Karenia selliformisand Alexandrium minutumin the Boughrara lagoon exhibited significant variability at annual scales. K. selliformiswas recorded in all sampling years with interannual variability. Among the nine sampled years, 2010, 2012, 2016 and 2017 were, respectively, the most significant in terms of mean abundance (2.85, 2.42, 1.38, 1.69) ∙ 105cells L–1. A. minutumspecies were observed in the water column during all investigated years except in 2013, 2016 and 2017, but in low concentrations compared to K. selliformis(≤ 7.4 ∙ 102cells L–1). Using LC-FLD, traces of paralytic toxins (C1 and GTX-2) were detected in some clam samples. Their concentrations were largely below the regulatory limit. For the first time, N-sulfocarbamoyl gonyautoxin-2 (C-1) and gonyautoxin 2 (GTX-2) were detected in some clam samples from this region. LC-MS/MS analysis confirmed the presence of gymnodimines in some samples. The main peak corresponds to the GYM-A with high concentrations generally above 1 mg kg–1of clams meat, which confirms the persistence of this neurotoxin in Boughrara lagoon.