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International trade increases connections and dependencies between countries, weaving a network of global supply chains. Agricultural commodity trade has implications for crop producers, consumers, crop prices, water and land uses, and other human systems. Interconnections among these systems are not always easy to observe when external impacts penetrate across multiple sectors. To better understand the interactions of non-linear and globally coupled agricultural-bioenergy-water systems under the broader economy, we introduce systematic perturbations in two dimensions, one human (restrictions on agricultural trade) and the other physical (climate impacts on crop yields). We explore these independently and in combination to distinguish the consequences of individual perturbation and interactive effects in long-term projections. We show that most regions experience larger changes in cereal consumption due to cereal import dependency constraints than due to the impacts of climate change on agricultural yields. In the scenario where all regions ensure an import dependency ratio of zero, the global trade of cereals decreases ~50% in 2050 compared to the baseline, with smaller decreases in cereal production and consumption (4%). The changes in trade also impact water and bioenergy: global irrigation water consumption increases 3% and corn ethanol production decreases 7% in 2050. Climate change results in rising domestic prices and declining consumption of cereal crops in general, while the import dependency constraint exacerbates the situation in regions which import more cereals in the baseline. The individual and …