The operation of a ships propulsion system is a variable process in time, which is described in both static and dynamic states. The mutual proportions between them depend primarily on a type of ship and tasks to which it was designed. In a case of special units of particular use (e.g. warships) and ships, which operate on narrow waters such as canals or port basins, participation of dynamic states is increasing significantly. Hence a necessity to analyze the dynamic states of marine diesel engines, among others in terms of their increased harmful compounds emission. The paper presents a methodology of engine dynamic state analysis, emission indicators that can be used to assess the dynamic state of a ship have been proposed. As an example of application, the analysis of harmful compounds emissions during dynamic states while a real cruise of navy ship has been carried out. It has been also proposed to use simple dynamics indicators such as single-base and chain indexes to describe the change in concentrations of harmful compounds in dynamic states.