Common rail systems are a key component of modern diesel engines and highly increase their performance. During their working lifetime, there could be critical damages or failures related to aging, like backlash or friction, or out-of-spec operating conditions, like low-quality fuel with, e.g., the presence of water or particles or a high percentage of biodiesel. In this work, suitable data-driven methods are adopted to develop an automatic procedure to monitor, diagnose, and estimate some types of faults in common rail systems. In particular, the pressure control loop operating within the engine control unit is investigated; the system is described using a Hammerstein model composed of a nonlinear model for the control valve behavior and an extended linear model for the process dynamics, which also accounts for the presence of external disturbances. Three different sources of oscillations can be successfully detected and quantified: valve stiction, aggressive controller tuning, and external disturbance. Selected case studies are used to demonstrate the effectiveness of the developed methodology.