To assess the sustainability of rice production systems, it is essential to quantify its impact on the environment and energy flow. To analyze the energy flow and greenhouse gas emissions, a total of 200 paddy fields were selected based on the water source utilized for irrigation (river as the surface water source and well as the underground water source), transplanting methods (traditional and mechanical) and grain yield (low‐ and high‐yielding rice cultivars) based on a factorial experimental design (2 × 2 × 2 = 8 conditions). Data were collected in 2020 from 200 rice growers in northern Iran, using a face‐to‐face questionnaire survey. Results showed that the highest total energy use efficiency (EUE) (5.26 GJ ha−1) was observed under the surface water source + traditional + low‐yielding rice system. Although the total EUE in surface water source was higher than that in groundwater source (4.98 vs. 2.90). Water consumption by high‐yielding rice cultivars was higher, as compared to the low‐yielding ones. Electricity (35.2%) and nitrogen fertilizer (31.5%) inputs were the highest energy input for the groundwater and surface water sources, respectively. Average shares of the renewable and non‐renewable energies used in agroecosystems were 25.70% and 74.30% respectively, while the shares of the direct and indirect energies were 60.36% and 39.64%, respectively. The calculated global warming potential value in the paddy fields of northern Iran ranged from 878 to 2,666 kg eqCO2 ha−1. Amongst the studied conditions, the surface water source + traditional + high‐yielding rice system had the highest carbon efficiency and carbon sustainability index level. Overall, surface water source conditions were found to be a more environmentally‐friendly approach in northern Iran. These results, thus, demonstrated that there is a huge potential for improving energy efficiency in the studied conditions, especially for high‐yielding rice cultivars irrigated by surface water sources. These findings could help decision‐makers to better understand the linkage between various conditions, which is a prerequisite to any planning effort for future management strategies at national and international levels.