Localized catalyst activity in an SCR unit for controlling emissions from a boiler, power plant, or any facility that generates NOx-containing flue gases is monitored by one or more modules that operate on-line without disrupting the normal operation of the facility. Each module is positioned over a designated lateral area of one of the catalyst beds in the SCR unit, and supplies ammonia, urea, or other suitable reductant to the catalyst in the designated area at a rate that produces an excess of the reductant over NOx on a molar basis through the designated area. Sampling probes upstream and downstream of the designated area draw samples of the gas stream for NOx analysis, and the catalyst activity is determined from the difference in NOx levels between the two probes.