Aquaculture farms have been established along the South Sea Coast of Korea, supplying most of the seafood consumed domestically. However, annual harmful algal blooms pose a potential threat to seafood safety. This study aimed to determine the spatial and seasonal distributions of 12 lipophilic marine biotoxins (LMTs) in phytoplankton and mussels in the region in 2021. Solid-phase adsorption toxin tracking (SPATT) was used to monitor the cumulative compositions of LMTs in seawater. LMT concentrations were also determined in twelve commercially available species of domestic shellfish to evaluate the potential risks to human health. Gonyaulux spinifera and Dinophysis acuminata, causative microalgae of yessotoxins (YTXs) and pectenotoxins (PTXs), respectively, showed high densities in the region from May to July. This period corresponded to high LMT concentrations in phytoplankton and mussels. Phytoplankton mainly contained PTX-2 and homo-YTX, with a maximum concentration of 2300 ng g−1 wet weight (ww) in May. In contrast, mussels mainly contained homo-YTX and YTX, with a maximum concentration of 1300 ng g−1 ww in July. LMTs-producing microalgae showed low densities and concentrations after July, whereas mussels accumulated toxins until September. In the SPATT sampler, more diverse LMTs were detected than in seawater, phytoplankton, and mussels. For example, dinophysistoxin-1 and azaspiracid-2 were detected only in SPATT. YTXs were detected in domestic seafood samples, including mussels, red scallops, and pen shells, but the concentrations were below the European Food Safety Agency recommended standard of 3.75 mg YTX-eq. kg−1. Moreover, the hazard quotient was less than 100 in all scenarios, indicating that the human health risk was not significant. This study provides valuable data on monthly distribution patterns of LMTs in the South Sea Coast of Korea and can serve as baseline data for future management policies of marine biotoxins.