This study examines the impact of NAFTA and USMCA free trade agreements on trade deficits and net agricultural trade between the United States, Canada, and Mexico, focusing on HS6-digit level agricultural commodities from 1994 to 2020. Using ARDL and gravity models, the results show that NAFTA led to increased trade volumes and improved net trade positions—particularly for Mexico, whose net agricultural trade surplus with the U.S. grew by approximately 24%. In contrast, the United States experienced a 15% increase in its agricultural trade deficit under USMCA, while Canada’s balance remained relatively stable, with fluctuations within a ±5% range. The ARDL model indicates that GDP (β = 0.47, p < 0.01), exchange rate (β = 0.82, p < 0.05), and government spending (β = –0.39, p < 0.1) significantly influenced bilateral trade deficits. In the gravity model, GDP per capita had the strongest positive effect on net agricultural trade (β = 1.75, p < 0.01), while agricultural value-added had a negative impact (β = –0.61, p < 0.05). These findings suggest that structural changes in trade agreements, combined with macroeconomic conditions, have measurable effects on national trade balances. For countries like Iran, the study highlights the importance of designing bilateral trade frameworks that promote agricultural competitiveness, maintain exchange rate stability, and protect vulnerable producers. Evidence-based trade policy can help Iran achieve greater trade resilience and improve its position in regional agricultural markets.