Community concerns about environmental issues and scarcity of water in major cotton-growing areas in Australia have stimulated the industry to improve on-farm water-use efficiency and productivity. Governments and industry have made considerable investments to improve water-management outcomes. The data presented in this paper confirm that the research and development investments and activities of farmers in irrigation improvement projects have paid excellent dividends. For scientists, it shows the positive outcomes of previous research projects and opens up new avenues for further research.

Review of a large body of research into the deep drainage component of the soil water balance, in the northern Australian cotton industry and globally, indicates large losses for furrow irrigation on a wide variety of soils, including most cracking clays. This can be halved with proven, available management changes. Deep drainage leachate is typically saline, can cause large losses of nitrate, and is not a source of good quality groundwater recharge.

Over a period of nineteen years, the three CRCs dedicated to the science of cotton production systems provided a strong focus for research into the characterisation, distribution, physical and chemical condition, prevalence of salinity and sodicity, and soil carbon and biotic status of Vertosols. Outcomes from much of this applied research were fed back to the industry through contributions to extension and education materials, while the discipline of soil science also benefitted through advances in measurement and mapping methodologies.

In 1990, water quality was seriously compromised in Australian river catchments where cotton was king.  How this dire situation was remedied during 20 years of research and practice in developing ‘the cotton model’ for environmental protection with world impact is described in this review.  The success now shown by integrated best practices was only possible because of a cooperative venture by a cast of thousands of researchers, local communities and cotton farmers.

Black root rot, a seedling disease reaching the level of an Australian pandemic, is caused by the soil-borne fungal pathogen Thielaviopsis basicola, a species with a worldwide distribution.   This review covers issues related to black root rot spread, severity and management, including the biology and ecology of T. basicola, host range and specificity, chemical and biological control of T. basicola in cotton cropping systems, crop rotations and host resistance. Although this review is mainly focusing on Australian cotton production systems, its wide scope makes it beneficial for readers worldwide.

Reviewed was the research coordinated by the Australian Cotton Cooperative Research Centre that investigated production issues for the future reintroduction of irrigated cotton to tropical Australia. The climatic and pest threats to cotton production were investigated with the aim of defining the potential limitations and where appropriate building a sustainable technical foundation for a future industry. It was demonstrated these limitations can be overcome by developing a deep understanding of the pests and climate then tailoring and validating production practices.

Groundwater is an important contributor to irrigation water supplies. The time lag between withdrawal and the subsequent impacts on the river corridor presents a challenge for water management. We highlight aspects of this challenge by examining trends in the streamflow and groundwater levels for the Namoi Catchment within the Murray–Darling Basin, Australia. The results show that further research is required on the delivery and usage of surface-water and groundwater, at different times and to different locations, to achieve both goals of supporting irrigated agriculture and protecting groundwater-dependent ecosystems.

Furrow irrigation of cotton on cracking clay soils has the potential to generate large amounts of drainage that wastes water and can cause saline watertables to rise. A lysimeter was installed under a cotton-wheat rotation to accurately measure drainage and other aspects of soil water. Most drainage occurred within a few days of irrigation and was caused by rapid flow of water down large pores that bypassed the soil matrix, rather than by the slower movement through the matrix.

Subsurface drip irrigation (SDI) has increasingly been employed as a means to improve irrigation water-use efficiency and yield; however, its performance in cotton production systems has not been encouraging. Oxygation of SDI has consistently delivered significant gains in both water-use efficiencies and yield.

Coarse sediments from palæochannels can cause high irrigation water losses as we confirmed with field data and numerical modeling. However, the irrigation water losses are not due direct infiltration in the coarser sediment, but through lateral flows from surrounding clay soils.

Groundwater ecosystems provide important services in maintaining groundwater quality and flow, as well as supporting numerous surface ecosystems. To better understand groundwater ecosystems and potential human impacts on them, we studied the biota within two adjacent alluvial aquifers, showing that the communities were functionally similar and responded to similar environmental factors. These similarities in biota and ecosystem functioning, suggest that management, assessing and monitoring of groundwater ecosystems may not require catchment specific targets or approaches.

Land-use change has resulted in large amounts of carbon (C) being released to the atmosphere. This study quantifies the substantial C store in subhumid and semi-arid floodplain ecosystems in inland Australia. While C sequestration has monetary value under the Kyoto agreement, this study suggests the need for financial remuneration to protect existing C stores and ensure that vegetation degradation and release of additional C to the atmosphere do not occur.