An engine protection system and methods for preventing intake condensation are disclosed. In a system and various of the methods, an exhaust gas recirculation (EGR) valve is positioned within an EGR passage fluidly connecting an engine exhaust stream and an engine intake stream, while a waste heat recovery (WHR) system is used to recover heat from the EGR stream. An engine control unit (ECU) is coupled to various sensors and valves to divert working fluid from the WHR system from cooling the EGR exhaust flow below a level which favors production of condensation in the engine intake system. The ECU operates to divert working fluid flow when sensors indicate characteristics of either the exhaust flow or the intake stream which might lead to heavy condensation. A three-way valve is also used to divert the working fluid to a variable expansion valve fluidly coupled to the three-way valve in response to a signal from one of the sensors to prevent damage to the system turbine.