The influence of using biodiesel fuels on the hydraulic behavior of a solenoid operated common rail injection system has been explored by means of a one-dimensional model. This model has been previously obtained, including a complete characterization of the different components of the injector (mainly the nozzle, the injector holder and the electrovalve), and extensively validated by means of mass flow rate results under different conditions. After that, both single and multiple injection strategies have been analyzed, using a standard diesel fuel and rapeseed methyl ester (RME) as working fluids. Single long injections allowed the characterization of the hydraulic delay of the injector, the needle dynamics and the discharge capability of the couple injector-nozzle for the two fuels considered. Meanwhile, the effect of biodiesel on main plus post injection strategies has been evaluated in several aspects, such as the separation of the two injections or the effect of the main injection on the post injection fueling. Finally, a modification in the injector hardware has been proposed in order to have similar performances using biodiesel as the original injector configuration using standard diesel fuel.