The present invention controls reagent flow levels in a selective non-catalytic reduction (SNCR) system by more accurately predicting Nitrogen Oxides (NOx) production with a municipal waste combustor. In one embodiment, the reagent levels correspond with measured furnace temperatures. The reagent levels may have a baseline level from prior measured NOx that is then modified according to temperatures measurements. A slow controller may use NOx measurements over an extended period to define a base regent level, and a fast controller may use additional information such as the furnace temperature to modify the base regent level. The fast controller may further receive two additional signals that are added individually or together to maximize NOx control while minimizing ammonia slip from the reagent. The two signals are a feed-forward signal from the combustion controller and a feedback signal from an ammonia analyzer downstream of the combustion zone.