Shipping represents a significant source of diesel emissions, which affects global climate, air quality and human health. As a solution to this problem, biodiesel could be used as marine fuel, which could help in reducing the negative impact of shipping on environment and achieve lower carbon intensity in the sector. In Southern Europe, some oily wastes, such as wastes from olive oil production and used frying oils could be utilized for production of the second-generation biodiesel. The present research investigates the influence of the second-generation biodiesel on the characteristics of gaseous emissions of NOx, SO2, and CO from marine diesel engines. The marine diesel engine that was used, installed aboard a ship, was a reversible low-speed two-stroke engine, without any after-treatment devices installed or engine control technology for reducing pollutant emission. Tests were carried out on three regimes of engine speeds, 150 rpm, 180 rpm and 210 rpm under heavy propeller condition, while the ship was berthed in the harbor. The engine was fueled by diesel fuel and blends containing 7% and 20% v/v of three types of second-generation biodiesel made of olive husk oil, waste frying sunflower oil, and waste frying palm oil. A base-catalyzed transesterification was implemented for biodiesel production. According to the results, there are trends of NOx, SO2, and CO emission reduction when using blended fuels. Biodiesel made of olive husk oil showed better gaseous emission performances than biodiesel made from waste frying oils.