The growing demand for private and public transport services in urban areas requires sophisticated approaches to achieve satisfactory mobility standards in urban areas. Some of the main problems in urban areas today are road congestions and consequently vehicle emissions. The aim of this paper is to propose a methodological approach for the estimation of vehicle emissions. The proposed methodology is based on two interrelated models. The first model is a microscopic simulation SUMO model which can be used to identify the most congested urban areas and roads with critical values of traffic parameters. The second model is the COPERT Street Level for estimating vehicle emissions. The proposed models were tested on the urban area of Rijeka. The results of the microscopic SUMO simulation model indicate six urban roads with the critical traffic flow parameters. On the basis of the six identified urban roads, an estimation of vehicle emissions was carried out for specific time periods: 2017, 2020, 2025, and 2030. According to the results of the second model, the urban road R20-21 was identified as the most polluted road in the urban district of Rijeka. The results indicate that over the period 2017–2030, CO emissions will be reduced on average by 57% on all observed urban roads, CO2 emissions by 20%, and PM emissions by 58%, while the largest reduction of 65% will be in NOx emissions.