Lipophilic shellfish toxins (LSTs) produced by dinoflagellates, including Dinophysis spp., can accumulate in bivalves. The seasonal variability of LSTs in bivalves and waters, and the abundance of Dinophysis spp. were investigated in Jinhae Bay, Republic of Korea, in 2007. Diarrhetic shellfish poisoning (DSP) such as okadaic acid and dinophysistoxin-1, and other lipophilic toxins such as pectenotoxin-2 (PTX2) and yessotoxin were analyzed by liquid chromatography—tandem mass spectrometry (LC-MS/MS). The toxin concentration in size-fractionated plankton material (20–100 µm in size) concentrated from a specific volume of water was converted into the toxin contents per unit volume of water. Among the genus Dinophysis, only D. acuminata was observed. The seasonal variability of okadaic acid, dinophysistoxin-1, and PTX2 per unit volume of water paralleled that of the abundance of D. acuminata. The cellular content and profile of toxins in D. acuminata varied, but PTX2 was mostly the dominant toxin. The toxins in the hepatopancreas of mussels (Mytilus galloprovincialis) were found from spring to autumn, and relatively high levels of toxins were detected in summer (June to August). Variation of the toxins in the hepatopancreas of mussels was remarkably consistent with both abundance of D. acuminata and toxin concentration in the water. Our results suggest that LC-MS/MS analysis of toxin in plankton concentrates has the possibility of becoming an alternative to or complement of the conventional microscopic method in toxic phytoplankton monitoring.