Ship emissions are a major cause of global air pollution, and in particular, emissions from the combustion of bunker fuels, such as heavy fuel oil (HFO), show strong impacts on the environment and human health. Therefore, sophisticated measurement techniques are needed for monitoring. We present here an approach to remotely investigating ship exhaust plumes through onboard measurements from a research vessel in the Baltic Sea. The ship exhaust plumes were detected from a distance of ~5 km by rapid changes in particle number concentration and a variation in the ambient particle size distribution utilizing a condensation particle counter (CPC) and a scanning mobility particle sizer (SMPS) instrument. Ambient single particles in the size range of 0.2–2.5 μm were qualitatively characterized with respect to their chemical signature by single-particle mass spectrometry (SPMS). In particular, the high sensitivity of the measurement method for transition metals in particulate matter (PM) was used to distinguish between the different marine fuels. Despite the high complexity of the ambient aerosol and the adverse conditions at sea, the exhaust plumes of several ships could be analyzed by means of the online instrumentation.