Nitrate is a crucial element for crop growth, and its optimal application is essential for maximizing agricultural yield. In Iranian agriculture, there is a substantial gap between recommended nitrate usage and what farmers actually apply. In this study, our primary objective is to determine the most effective utilization of nitrate for crop cultivation. Simultaneously, we aim to analyze the factors that contribute to the disparity between optimal and current nitrate application practices. Furthermore, our research explores the impact of these differences on regional variations in crop yields. This is achieved using a quadratic yield response function model based on unbalanced panel data spanning the years 2000 to 2016, which includes a total of 14 crop activities and encompasses 31 administrative regions. The results show that rice exhibits the highest nitrogen usage, while rain-fed wheat demonstrates the lowest utilization at the optimal point. Depending on whether random- or fixed-effects estimation is found to be the most suitable specification, average yields corresponding to the optimal level of nitrogen use are calculated by region, or the average across all regions. In Iran, the top-performing regions for cereals like rain-fed wheat and irrigated barley can achieve yields of 1.33 and 3 t/ha, respectively. These yields represent a 31% and a 9% increase from the levels observed in 2016. The outcomes derived from the estimated yield response function will be integrated into comprehensive agricultural, economic, and environmental optimization models. These integrated models will facilitate the assessment of various fertilizer policies on fertilizer use, land allocation, farm-household incomes, and environmental externalities, such as nitrate leaching and nitrate balance. This study holds substantial scientific promise, given its exploration of the policy implications surrounding fertilizer usage, making it crucial not only for Iran, but also for many developing nations grappling with inefficient and unsustainable agricultural practices. It represents the first of its kind in the literature, providing estimations of optimal nitrogen use and crop yield points across all regions in Iran. This is achieved through advanced visualization using GIS maps.