Wheat crops face various biotic and abiotic stresses, with waterlogging being a major abiotic factor negatively impacting productivity worldwide. The severity of waterlogging has increased due to unexpected and drastic climate changes, especially the rise in unseasonal heavy rainfall over the past two decades in irrigated and high-rainfall areas. Waterlogging causes multiple problems for wheat growth and yield, including restricted gas exchange, nutrient deficiencies, and microelement toxicities. Its effects vary depending on depth, duration, plant growth stage, and weather conditions. Waterlogging reduces tiller number, spike number, grains per spike, and grain weight, leading to significant yield loss. The situation worsens when waterlogging occurs during crop lodging, particularly around heading or later stages. Wheat plants develop morphological, physiological, and metabolic adaptations to survive waterlogged conditions. The negative effects of waterlogging can be mitigated through suitable agronomic, breeding, and biotechnological strategies. Practices such as raised-bed cultivation, laser land levelling, and nutrient management have proven effective, along with breeding approaches. Many studies have identified promising genotypes, QTLs, and traits associated with waterlogging tolerance, enabling rapid development of tolerant cultivars through high-throughput phenotyping. This chapter reviews recent progress in agronomic, breeding, and genomic methods to address waterlogging stress, aiming to sustain annual productivity and improve resilience in future wheat varieties amid ongoing climate challenges.