The interest in water-diesel emulsion fuel (EM) is increased recently because of the significant reduction in emissions from diesel exhaust, especially NOx and PM. In this study, a diesel engine configured for experimental investigations was fueled by ultra-low sulfur diesel (ULSD) and a diesel-water emulsion (EM). Both fuels’ combustion characteristics were studied at a speed of 1500 rpm and using a load of 2.5 and 5 bars and variable injection timings. Regular and irregular pollutants were studied at the same conditions as well as at variable engine loads and speeds to better understanding for their formation conditions. As for the first time (in the case of an engine running with a water-diesel emulsion) irregular pollutants for EM emulsion were measured.The measured results indicated that the use of water-diesel emulsion reduced the heat released in the combustion chamber, which causes an increase in the brake specific fuel consumption and ignition delay. For the tested loads, the diffusion combustion duration for EM was decreased when the injection timing was retarded while the opposite was occurred for premixed combustion duration. The regulated NOx and Smoke Number were reduced when EM was used compared to ULSD while CO and HC levels were increased at low engine’s speed and loads. Besides, these concentrations are depending on injection timing (they were higher at restarted timing). The unregulated emissions measured (Formaldehyde, Acetaldehyde, Methane, Acetylene, Ethylene, and propylene, Ammonia, and Acetone) were increased with using EM, especially at no and low loads, indicating the high impact of the combustion chamber temperature on these pollutants formation.