Bivalve mollusk production represents the principal aquaculture activity in Sardinia (40°03′ N, 9°05′ E). In 2021, 859 water samples and 1270 mollusk samples were analyzed. The species Alexandrium minutum caused the accumulation of Paralytic Shellfish Toxins (PST) in three samples of bivalve mollusks. Dinophysis acuminata complex caused the accumulation of lipophilic toxins (LTs) belonging to the okadaic acid group (OAs) in 18 samples of bivalve mollusks. The research of paralytic shellfish toxins (PSTs) in shellfish samples has been carried out with LC-FLD, as mentioned in the AOAC 2005 Official Method 2005.06. The determination of LTs was carried out by LC-MS/MS analysis. DTX2, belonging to the group of OA toxins, was detected for the first time in Sardinia, in mussels sampled in Tortolì. The presence of Dinophysis and Prorocentrum species was correlated with the accumulation of the OA toxin group in bivalve mollusks, showing a certain repeatability at certain times of the year in the areas included in the study. The results of the present study can help to plan and organize more effective bio-monitoring sampling strategies.