This study investigates the spatial and seasonal distribution of potentially harmful dinoflagellates (PHDs) and their environmental drivers in the coastal waters of Songkhla Province, Thailand. Sampling was conducted across five stations: two semi-enclosed coastal areas (Site A: A1 and A2) and three exposed coastal areas (Site B: B1, B2 and B3). The sampling period, from July 2023 to March 2024, covered the Southwest Monsoon (SWM), Northeast Monsoon (NEM), and Intermediate Dry (IMD) seasons. Twelve PHD species were identified. Seven species (Noctiluca scintillans, Dinophysis caudata, D. miles, Tripos furca, T. fusus, T. tripos, and T. trichoceros) were detected consistently across all sites. Noctiluca scintillans and T. furca were the most abundant and widespread across all sites and seasons. ANOVA revealed significant seasonal effects on the abundance of D. caudata, D. miles, and T. macroceros, while T. fusus showed significant spatial variation (p < 0.05). Canonical Correspondence Analysis (CCA) indicated that dissolved oxygen (DO), pH, temperature, and nitrite concentrations were key variables influencing PHD distribution. Diversity was higher at Site B (H′ = 1.45, E = 0.61, S = 11) than at Site A (H′ = 1.30, E = 0.54, S = 11). Low DO and high nutrient levels in semi-enclosed areas were associated with freshwater inflows and aquaculture activity, whereas exposed coastal stations showed greater physicochemical stability but remained sensitive to nutrient enrichment during the NEM and IMD seasons. Integrated statistical analyses underscored the role of both monsoonal hydrodynamics and anthropogenic nutrient loading in regulating harmful dinoflagellate assemblages along the Songkhla coast. The findings emphasize the importance of site-specific, seasonally adaptive monitoring to the management of coastal water quality and mitigation of harmful algal blooms. The insights provided into the ecological dynamics of tropical coastal systems can inform future strategies for sustainable coastal zone management and support the aims of Sustainable Development Goal (SDG) 14: Life Below Water.