Soybean and wheat are important crop species due to their significance for human consumption, animal feed, and industrial use. However, increasing global population and worsening climate change have put a major strain on the production system of these crops. Natural disasters such as flooding and drought can severely impact growth and productivity of these crops. In addition, increased application of synthetic nitrogenous fertilizers to meet the global food demand has led to environment related issues. Therefore, with a goal of understanding mechanisms of flooding and drought tolerance in soybean and nitrogen-use-efficiency in wheat, we explored their physiological and transcriptomic regulation. We characterized the fundamental acclimation responses of soybean to flooding and drought and compared the metabolic and transcriptomic regulation during the stresses in a tissue-specific manner. We demonstrated the dynamic reconfiguration of gene expression and metabolism during flooding, drought, and recovery from these stresses. Our study displayed that flooding triggers more dramatic adjustments than drought at the transcriptional level. We also identified that the soybean genome encodes nine members of group VII ERF genes and characterized their responses in leaves and roots under flooding and drought. Based on the expression patterns, it is estimated that two of the nine genes are promising candidate genes regulating tolerance to submergence and drought. In addition, our genome-scale expression analysis discovered commonly induced ERFs and MAPKs across both stresses (flooding and drought) and tissues (leaves and roots), which might play key roles in soybean survival of flooding and drought. In wheat, we evaluated the effect of three different nitrogen rates on yield and its components across four diverse soft red winter wheat genotypes. The cultivar Sisson displayed superior performance in grain yield and nitrogen use efficiency at low nitrogen levels. Our results suggested that improvement of nitrogen use efficiency in low nitrogen environments can be achieved through the selection of three components: grain number/spike, 1000-seed weight, and harvest index. Overall, this study has advanced our understanding of how plants respond to abiotic stresses such as flooding, drought, and nutrient limitation conditions. / Ph. D. / Soybean and wheat are commercially important crop throughout the world. Soybean is a major source of protein and oil for humans, livestock and industrial products including biofuel production. Similarly, wheat is a major source of food products such as bread, pasta, and cookies. However, increasing global population and worsening climate change have put a major strain on the production system of these crops. Natural disasters such as flooding and drought are on the rise, which have severely impacted soybean growth and productivity. In addition, increased application of synthetic nitrogenous fertilizers in wheat production to meet the global food demand has led to environment related issues. Therefore, a mechanistic understanding of flooding and drought tolerance in soybean and nitrogen use efficiency in wheat is of utmost importance. The knowledge obtained from these studies can aid in the development of new varieties in these crops. Here, we carried out our study on soybean by imposing either complete submergence or restricting water supply to characterize the responses to these stresses in shoot and root systems. We found several compounds and genes that were altered distinctly under these two water-related stresses. In addition, we identified some promising genes that can significantly regulate tolerance in soybean to flooding and drought in soybean. To study wheat nitrogen use efficiency, we selected four diverse soft red winter wheat varieties and grew them under three nitrogen levels. We found that the cultivar Sisson has the lowest yield penalty among the four varieties resulting from low nitrogen conditions. In addition, we also demonstrated that three yield traits (grain number per spike, 1000-seed weight, and harvest index) are important selection targets to develop high nitrogen use efficiency varieties.