Complex research into the change of parameters concerning the fuel economy, thrust, and harmful components of exhaust gases, namely, hydrocarbons (HQ, carbon monoxide (CO), and nitric oxides (NOx), was carried out to evaluate the efficiency of fuel replacement; that is, mineral diesel fuel, which is normally used by diesel engine fleets of agricultural machinery in Lithuania, was replaced with biofuel (hereafter biodiesel), which is rapeseed oil methyl esters, hereafter RME. Diesel engine F2L511 and a single section of diesel engine A41 were chosen as models and tested within the above-mentioned research parameters. Fuel blends of mineral diesel fuel and RME-biodiesel fuel, and also pure RME, were tested as follows: 1310, in which the content of RME is 10%; B 15 and 1330, in which the contents of RME are 15% and 30% appropriately; and 13100, which is pure RME. A nonlinear change of operational characteristics was determined depending on the loads of the diesel engine. According to its technical ecological parameters, B30-biodiesel fuel was acknowledged as the most convenient and reliable one being tested within a wide range of speed and load regimes. In the same range of speed and load regimes, the influence of technical conditions of the fuel injector on harmful emission parameters of diesel engine exhaust gases, while running on RME, was estimated by means of a failure simulation of the fuel injector, namely, gumming up the fuel injector nozzle. An improvement of all the ecological parameters was estimated by optimization of the diesel engine injection timing while running on RME.