A nonlinear control approach of an innovative engine cooling system for vehicles is presented in this paper. The electrically driven coolant pump and a servo-controlled bypass valve as control inputs, however, are subject to saturation due to physical limitations of the maximum pump volume flow and the limited opening section of the bypass valve. Based on a control-oriented system representation, a decoupling, input-output-linearising control is designed for the engine outlet temperature and the engine inlet temperature. At this control design, the given actuator limitations are explicitly taken into account. The multi-variable control is implemented with a small sampling time and combined with a discrete-time Extended Kalman Filter that estimates unknown heat flows within the system. Experimental results from a dedicated test rig highlight the effectiveness and the performance of the proposed control approach.