A system includes a selective catalytic reactor and a bypass line. The selective catalytic reactor is located downstream of a furnace that generates flue gases. The selective catalytic reactor reduces nitrogen oxides to nitrogen. The bypass line is in fluid communication with the selective catalytic reactor. The bypass line contacts an input line to the selective catalytic reactor, where the bypass line is adapted to handle a volume of flue gases diverted from the selective catalytic reactor. A first control damper is disposed at an inlet to the selective catalytic reactor; and a second control damper is disposed at an inlet to the bypass line. The first control damper and the second control damper interact to divide the flue gas stream between the selective catalytic reactor and the bypass line in a ratio to reduce the amount of sulfur trioxide released from the system to a desirable value.