Harmful algal blooms have been documented in the Moroccan Western Mediterranean region since 1993, primarily associated with the presence of paralytic shellfish toxins (PSTs) produced by the dinoflagellate Gymnodinium catenatum. The proliferation of this neurotoxic species has led to recurring bans on the harvesting of molluscs, resulting in significant socio-economic repercussions and threats to human health. In the present study, we examine the dynamics of G. catenatum and mollusc PST contamination patterns over a 20-year period (2002−2021) in two distinct marine ecosystems: M'diq Bay and the Oued Laou Estuary. For the PST contamination, we considered two commercially important shellfish species: the smooth clam, Callista Chione, and the cockle, Acanthocardia tuberculata. The highest G. catenatum abundances were consistently observed from November to February in both sites. Our data revealed inter-annual variations in G. catenatum abundance, peaking at 91,840 cells.L−1 in November 2011. PST contamination levels in A. tuberculata were significantly higher than those observed in C. chione. Furthermore, we identified a significant correlation (Pearson, P-value \textless0.05) between PST contamination of smooth clams and the abundance of G. catenatum. The contamination of A. tuberculata by PSTs reached very high levels, with up to 13,500 μg STX di-HCl eq. kg−1 of shellfish meat, exceeding the established safety thresholds by 16-fold. Additionally, there has been an increase in the prevalence and incidence of PSTs over the years. Notably, we observed a substantial increase in G. catenatum blooms and PST events in the Western Mediterranean during the last decade (2010−2021). The examined data suggest that rainfall could play a pivotal role in G. catenatum bloom dynamics by enriching marine waters with nutrients. The statistical model selection approaches indicated that nutrient concentrations (i.e., nitrate and phosphorus) were the most significant parameters for G. catenatum blooms in the studied area.