Contamination from water and particulate matter in diesel or aviation fuel can cause complications even under normal operating conditions. Fuel contamination becomes a major problem in air transportation, where engine flame-out due to injection system blockage or malfunction might have catastrophic consequences. The presence of contaminants in fuel has been linked to several incidents including commercial and military aircraft over the past decade. Unless they are detected and separated from the fuel, water or solid particles have several ways to reach the engine and cause troubles. Aviation fuel is commonly stored in large tanks and transferred frequently before it reaches the aircraft, increasing the risk for contamination. At the same time, gas bubbles may be present in the system. While harmless to the aircraft, gas bubbles have been the reason why contamination monitoring systems would fail, as the system would be triggered by gas bubbles, instead of detrimental contaminants. We developed a set of optical diagnostics to detect the presence of contaminants in fuel, and quantify their size and concentration. The system consists of a microscope imaging system, a multi-angle scattering diagnostic and an infrared line-of-sight extinction system. The objective of the microscope imaging system is to measure contaminants, producing particle size distributions that, in conjunction with the scattering data, provide real-time concentration measurements. The multi-angle scattering intensity information permits to separate the different kinds of particles; it is especially sensitive to detecting gas bubbles. While unable to separate water from the other types of particles, infrared extinction proved to be highly responsive at detecting water slugs, while providing redundant information about contamination levels. The different diagnostics enable the system to reliably measure concentrations for various particle types with unmatched measurement accuracy and precision.