An engine assembly includes an exhaust system having a first SCR catalyst, a second SCR catalyst in fluid communication with the first SCR catalyst, and an injector configured to inject reductant into the exhaust system. A controller is configured to estimate a first amount of ammonia stored in the first SCR catalyst and to estimate a second amount of ammonia stored in the second SCR catalyst. The controller is operatively connected to the injector and configured to control the amount of reductant injected by the injector. The controller controls the injector based on the first amount, the second amount, and a temperature of a substrate disposed in the second SCR catalyst.