Climatic variability, typified by erratic heavy-rainfall events can cause soil waterlogging and yield losses in irrigated cotton. This project investigated the physiological mechanisms of waterlogging damage to cotton crops and suggested strategies for increasing waterlogging tolerance. Field and glasshouse studies were conducted to study the interactive effects of waterlogging and shade on growth and yield of cotton crops. The data indicated that both waterlogging and shade can significantly damage cotton growth and yield. In addition, low incident light can exacerbate yield losses in moderately WL cotton crops but had limited effect on a severely WL crop. Cotton plants maintained growth and photosynthesis of the upper canopy leaves by re-mobilising nutrients from lower canopy leaves. Thus, yield reductions in WL crops were associated with the loss of young fruits from the lowest sympodial fruiting branches. To overcome this waterlogging-induced fruit abscission, an anti-ethylene agent aminoethoxyvinylglycine (AVG) was tested under glasshouse and field conditions. The data suggested that 125 g [ai] ha-1 of AVG applied at the early reproductive phase of cotton can significantly increase lint yield of WL and NWL cotton crops. The role of ethylene and AVG in regulating cotton yield was further explored in a series of glasshouse studies. These experiments indicated that accelerated ethylene production and photosynthetic inhibition as the major reasons for yield losses in WL cotton and the damage can be minimised by regulating ethylene and carbon metabolisms.