Methods for estimating the mass flow rate of NOx in an exhaust stream by correlating the level of NOx to an engine parameter. The level of NOx can be estimated as a function of engine power, of intake pressure, of exhaust temperature, as a function of the percentage of O.sub.2 in the exhaust stream, or as a combination of any of these. Once the level of NOx is approximately known, the exhaust system of the engine system can be modified to improve the removal efficiency of NOx and exhaust particulate matter from the exhaust stream. These methods for estimating the NOx mass flow rate can be used for an exhaust configuration that includes a lean NOx catalyst (LNC), a selective catalytic reduction (SCR) catalyst, or a lean NOx trap (LNT). A particulate filter can be present in the exhaust configuration.