Shipping, as the most efficient, cheapest, and most widespread mode of transporting goods, also generates significant exhaust emissions. This has led to the adoption of stringent regulatory restrictions on emissions from ship propulsion systems. Consequently, the education and training of marine engineers can significantly impact their understanding of how emissions are generated and their potential for reduction. The engine room simulator is an indispensable tool in the training of marine engineers. Since operating conditions and parameters have the greatest impact on NOx emissions, this forms the primary focus of this research. This study tests the accuracy and precision of the engine room simulator in simulating emissions and evaluating the influence of operating conditions on them. Furthermore, the implementation and testing of NOx emission reduction technologies are vital for promoting sustainable shipping, ensuring regulatory compliance, and training personnel to support environmentally conscious maritime operations. Using the example of a two-stroke marine diesel engine, the results obtained are compared with test bench data from similar engines. Special emphasis is placed on simulating the operation of a two-stroke diesel engine at low speed, or low load, where secondary NOx reduction methods cannot be used. Therefore, the simulator is tested using two available technologies: water–fuel emulsion and altering the fuel injection timing to reduce NOx emissions. The simulation results for the water–fuel emulsion show high accuracy in predicting NOx emission trends when changing the water content in the emulsion at nominal power. However, at low load, the results show significant deviations. Testing the effect of altering fuel injection timing under low load using the engine room simulator shows significant differences compared to available research. Nonetheless, research on NOx emissions in this engine mode is limited, presenting a potential area for further study. When comparing the results for nominal power operation, the simulation provides more accurate results, particularly in terms of the influence of fuel injection timing on NOx emissions. However, engine tests on the test bench still reveal more substantial changes in emissions than those obtained using the engine room simulator.