An excess of water is more harmful to plant growth, root growth and the uniformity of the plant population than a water deficit. Water is a crucial factor in the three basic stages of soybean development: germination, emergence and flowering/seed filling. Waterlogging is one of the biggest constraints to crop production and productivity in India and can occur at any stage in soybean. However, seeds and seedlings are damaged by waterlogging resulting in a significant reduction in grain yield. Seed yield and growth are significantly correlated at the seedling stage. In addition, the plant is under constant pressure due to changing environmental conditions and has difficulty withstanding these harsh, unpredictable and difficult situations. Membrane transporters are essential and play fundamental roles during waterlogging thereby facilitating cellular homeostasis and gaseous exchange, which support plant growth and development. This review highlights the genetic basis and mechanism of waterlogging tolerance in soybean and the role of climate in influencing the genetic makeup of the crop, paving the way for further development of improved soybean varieties. Simultaneously, the article highlights membrane transporters' importance in water-mediated stress in soybeans.