This research compares the air pollution (CO, CO2, HC, NOx, smoke), energy (brake-specific fuel consumption, thermal efficiency) and noise indicators of a compression ignition engine fueled by first-generation biodiesel (rapeseed methyl ester (RME)) and second-generation biodiesel (hydrogenated vegetable oils (HVO)), or conventional (fossil) diesel fuel blends. The concentration of first- and second-generation biodiesel in two-component blends with diesel fuel was up to 15% and 30% (RME15, RME30, HVO15, and HVO30); for comparison, the three-component blend of diesel fuel, HVO and RME (RME15–HVO15) was considered. The fuels’ physical and chemical properties were tested in a specialized laboratory, and the engine load conditions were ensured by the engine brake stand. Referring to ship power plants with constant-speed engines, detailed research was carried out in one speed mode (n = 2000 rpm). Studies have shown that two-component fuel blends with HVO are superior to conventional diesel fuel and two-component blends with RME in almost all cases. The HVO in fuel blends reduced fuel consumption up to 1.8%, while the thermal efficiency was close to that of fossil diesel fuel. In addition, a reduction in pollutants was observed: CO by ~12.5–25.0%; HC by ~5.0–12.0%; NOx by ~6.5%; smokiness by ~11–18% (two-component blend) and up to ~29% (three-component blend). The CO2 and noise characteristics were close to those of fossil diesel fuel; however, the trend of reduced smoke emission was clearly seen. A fundamental obstacle to the wide use of HVO can be seen, however, which is the price, which is 25–90% (depending on the EU country) higher than the price of conventional (fossil) diesel fuel.