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Cotton is a major world crop that is notoriously susceptible to waterlogging damage, particularly when cultivated on fine-textured soils. However, damage is also exacerbated because of inadequate acclimation of roots to low oxygen levels, and secondary effects on shoots. Despite the commercial importance of cotton, very little has been published when compared with waterlogged cereals. This review provides a comprehensive view of the constraints on cotton in low-oxygen conditions, including absence of aerenchyma and the inadequacy of fermentation to overcome waterlogging damage. We emphasise the possibilities of improved tolerance through management practices, manipulation of hormone pathways and gene technologies to modify perception and response to low-oxygen environments.