A simple method was developed for the determination of biogenic amines in aquatic food products using a reverse-phase high-performance liquid chromatography with postcolumn automatic o-phthalaldehyde derivatization and fluorescence detection. The linearity, repeatability, and recovery of the method for seven amines (tyramine, putrescine, cadaverine, histamine, agmatine, spermidine, and spermine) were evaluated. This optimized method was applied to detect biogenic amines in squid and white prawn during refrigerated storage. Sensory analysis, pH value, and total volatile base nitrogen value were combined to evaluate the freshness quality of these two raw materials. Agmatine and cadaverine in squid, cadaverine, and putrescine in white prawn were the most obviously changed amines during the storage at two different temperatures, and these biogenic amines could be the effective quality indicators for the freshness of the raw aquatic materials.