This paper discusses hardware-based methods for monitoring the operational parameters of marine diesel engines and online mathematical modeling techniques (digital twins) for calculating the emissions of CO2, NOx, soot, and other harmful pollutants. It is demonstrated that measuring and analyzing the engine's vibrational diagrams in parallel with gas pressure diagrams in the cylinders allows the evaluation of the actual fuel injection and gas distribution timings. The obtained data is used to refine the mathematical model of the engine's working process, which determines the engine's indicator parameters and power, as well as the emission of harmful substances that need to be monitored in compliance with current IMO requirements. The authors have accumulated experience in using the discussed hardware-based methods for diagnosing marine engines during operation. The hardware and software methods discussed have been implemented into a real-time system for in-service diagnostics of marine engines. The system is designed based on a modern dual-core controller with high performance and low power consumption, incorporating a high-speed ADC with sufficient capability to monitor the working process with a 0.1-degree crankshaft rotation resolution for all types of marine main and auxiliary engines. The system also utilizes wireless data transmission technology. A contemporary Android/iOS smartphone or tablet serves as the computational and graphical component of the system. This real-time system enables the utilization of all the advantages of parallel pressure and vibroacoustic analysis, including real-time determination of key operating parameters, identification of top dead center position, and evaluation of fuel delivery and gas distribution phases. Additionally, it harnesses the benefits of employing a digital twin—an online mathematical model of the engine cylinder's working process. These solutions will enhance diagnostic quality and, ultimately, improve the operational efficiency of marine engines by reducing operational costs and extending the period of reliable, trouble-free operation.