The paper describes the method of a sea boats online diagnostic with the use of the main and accompanying processes analyses. The paper concerns injection and combustion processes taking place in internal combustion engines of the military boats. Authors chosen vibroacoustic processes in the research to obtain the important diagnostic information on the above processes runs and their correctness in the sources of a drive of the HDV off-road water transport vehicles. The specified method of a digital data acquisition for dynamic processes in such combustion engines and sort of diagnostic parameters taken into account were basis of the required empirical research process and further signal analyses. High accuracy of the measurement methodology and process with additional conditions caused the authors could take the obtained signals to the parallel, combustion engineering and vibroacoustic engineering process, according to which they extract important information on the combustion processes runs and their problems. Identification of such problems and its type was helpful to build algorithm of the diagnostic assessment of such processes in the point of view of building diagnostic system for such military boats with the regime of the efficiency of the energy changes and emission control in the all exploitation period.