The qualitative and quantitative analysis of polycyclic aromatic hydrocarbons (PAHs) has been important for the environmental control of persistent organic pollutants for decades. Considering the potential risk of deterioration, degradation, and external pollution during transportation, the development of rapid and onsite detection of trace PAHs is in demand. Here, taking the advantage of high sensitivity of surface-enhanced Raman spectroscopy (SERS), we developed a shipboard instrument by combining a portable Raman instrument and a flow injection device, integrating the sample pretreatment and target detection step by step. The feasibility of the instrument was demonstrated by detecting trace benzo[a]pyrene from different water environments with the lowest detection concentration less than 1 µg/l. The reliable stability and repeatability indicate that in the case of emergency response, the developed flow injection analysis-SERS instrument is very promising for the quantitative and qualitative analysis of diverse organic pollutants other than PAHs in water environments.