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.