Among abiotic stresses, floods are the most hazardous environmental stress that harshly restricts crop productivity and has become a major problem globally. It may result from defective irrigation, heavy rainfall, and poor drainage, which leads to infertile lands and food shortages. The circumstances of climate alteration and existing agricultural practices failed to overcome this crisis, so to alleviate flood stress in susceptible species and environment, considering flooding effects on plant-associated microbes is imperative. Low oxygen supply occurs in flood stress and is a common constraint to the plant and its associated microbiomes. Moreover, the gaseous hormone like ethylene is synthesized rapidly under hypoxic conditions in leaves, and roots from its precursor ACC (1-aminocyclopropane-1-carboxylate) that arrest the plant growth development. However, the elongation of the root systems in the submerged plants was reported due to the decreasing level of ethylene hormone via ACC deaminase-producing PGPRs. The negative effects can be mitigated once the plant displays adaptive responses to increase oxygen uptake by certain beneficial microbes, such as mycorrhiza and/or endophytes. They have multiple plant growth-promoting traits like phosphate solubilization and siderophore production to improve crop productivity under waterlogging conditions. Initially, ethylene effects are promotive but later become inhibitory depending on immersion level and concentration of auxin. Therefore, this book chapter furtherly presents the role of microbiomes as a key module of flooding stress tolerance and improving plant health.