1. A system for controlling SCR performance in a boiler, the boiler including one or more generally cross sectional areas, each cross sectional area being characterized by one or more profiles of one or more conditions affecting SCR performance and being associated with one or more adjustable desired profiles of said one or more conditions during the operation of the boiler, the performance of the boiler being characterized by boiler performance parameters, comprising: a controller input for receiving a performance goal for the boiler corresponding to at least one of the boiler performance parameters and for receiving data values corresponding to boiler control variables and to the boiler performance parameters, said boiler control variables including one or more current profiles of said one or more conditions; a system model that relates one or more profiles of said one or more conditions in the boiler to the boiler performance parameters; an indirect controller that determines one or more desired profiles of said one or more conditions to satisfy the performance goal for the boiler, said indirect controller using the system model, the received data values and the received performance goal to determine the one or more desired profiles of said one or more conditions; and a controller output that outputs the one or more desired profiles of said one or more conditions.