A controller directs operation of an air pollution control (APC) system performing a process to control emissions of a pollutant. The process has multiple process parameters (MPPs), one or more of the MPPs being a controllable process parameters (CTPPs) and one of the MPPs being an amount of the pollutant (AOP) emitted by the system. A user input device identifies an optimization objective. A control processor determines a set point for at least one of the one or more CTPPs based on the current values of the MPPs and the identified optimization objective, and directs control of one of the at least one CTPP based on the determined set point for that CTPP.