The protection of air from pollution is one of the basic principles of sustainable development, and this article analyzes the joint impact of various types of agricultural production and traffic on nitrogen oxide (NOx) emissions. The goal of this research is the development of a new methodology for assessing the combined impact of different types of agricultural production, traffic load, and traffic flow structure on the emission of nitrogen oxides. For the analysis of the joint impact of traffic and agricultural production, a new impact assessment methodology was developed, which is based on two selected impact prediction models. The following two models were used to predict the impact: the BioGrace model and the microsimulation model VISSIM. The developed methodology was applied to a case study in real field conditions. The results showed that the difference in the emission of NOx gases, depending on the type of agricultural production, indicates a reduction in NOx emissions in the walnut–winter-wheat system by 30%, compared to the production of winter wheat in an open field. The statistical analysis showed that there is no statistically significant difference between NOx emissions for different vehicle arrival scenarios for the same traffic load. The results of the joint impact show that the lowest NOx emission was found in walnut orchards and counted traffic. In this example, the difference between the one-hour emission load of three different agricultural types of production and traffic is not large; however, in the cumulative load, it can lead to significant differences. Emphasizing the importance of adopting new agricultural practices and the impact of traffic and the share of freight and heavy goods vehicles in agricultural production, we position them as a proactive and sustainable response to the critical ecological and agricultural challenges highlighted in European and Croatian policy.