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Spirolides (SPXs), gymnodimines (GYMs), and pinnatoxins (PnTXs) have been detected in shellfish from the northwestern Mediterranean coast of Spain. Several samples of bivalves were collected from Fangar Bay and Alfacs Bay in Catalonia over a period of over 7 years (from 2015 to 2021). Shellfish samples were analyzed for cyclic imines (CIs) on an LC1200 Agilent and 3200 QTrap triple–quadrupole mass spectrometer. In shellfish, SPX-1 was detected in two cases (of 26.5 µg/kg and 34 µg/kg), and GYM-A was only detected in trace levels in thirteen samples. Pinnatoxin G (PnTX-G) was detected in 44.6% of the samples, with its concentrations ranging from 2 µg/kg to 38.4 µg/kg. Statistical analyses revealed that seawater temperature influenced the presence or absence of these toxins. PnTX-G showed an extremely significant presence/temperature relationship in both bays in comparison to SPX-1 and GYM-A. The prevalence of these toxins in different bivalve mollusks was evaluated. A seasonal pattern was observed, in which the maximum concentrations were found in the winter months for SPX-1 and GYM-A but in the summer months for PnTX-G. The obtained results indicate that it is unlikely that CIs in the studied area pose a potential health risk through the consumption of a seafood diet. However, further toxicological information about CIs is necessary in order to perform a conclusive risk assessment.