The PPSUITE program was developed for postprocessing travel demand model outputs to conduct transportation system performance and air quality conformity analyses by using the MOBILE6 vehicle emission modeling software of the Environmental Protection Agency. To account for the emissions caused by toll plaza congestion, a methodology of toll plaza delay estimation was developed as a component of PPSUITE's network operations module. This paper presents the development and application of that methodology. This tool provides a mesoscopic empirical method for estimating toll plaza delay in large-scale regional highway networks that can contain more than 100 toll plazas. The problem of analyzing each of these plazas for 24 h of the day would be impractically large or lacking in fidelity and accuracy without this tool. The methodology is also suitable for analyzing single toll plazas and time periods. In this methodology, toll plaza delay is calculated on the basis of the ratio of demand versus capacity (v/c) of the plaza for a payment type at a given time period. Depending on the v/c ratio, the plaza is in one of three states: free flow, transition, and queuing for the available payment types. Delays are calculated for these states considering the transaction times, vehicle composition, plaza approach geometry, lane use, and vehicle physical characteristics. With this methodology, a comparison of the delay estimates with estimates produced by VISSIM model of the New York-New Jersey Goethals Bridge toll plaza show that the delay methodology can accurately estimate delays for various v/c ratios.