The aim of this review is to report changes in irrigated cotton water use from research projects and on-farm practice-change programs in Australia, in relation to both plant-based and irrigation engineering disciplines.

At least 80% of the Australian cotton-growing area is irrigated using gravity surface-irrigation systems. This review found that, over 23 years, cotton crops utilise 6–7 ML/ha of irrigation water, depending on the amount of seasonal rain received. The seasonal evapotranspiration of surface-irrigated crops averaged 729 mm over this period. Over the past decade, water-use productivity by Australian cotton growers has improved by 40%. This has been achieved by both yield increases and more efficient water-management systems. The whole-farm irrigation efficiency index improved from 57% to 70%, and the crop water use index is >3 kg/mm.ha, high by international standards. Yield increases over the last decade can be attributed to plant-breeding advances, the adoption of genetically modified varieties, and improved crop management. Also, there has been increased use of irrigation scheduling tools and furrow-irrigation system optimisation evaluations. This has reduced in-field deep-drainage losses. The largest loss component of the farm water balance on cotton farms is evaporation from on-farm water storages.

Some farmers are changing to alternative systems such as centre pivots and lateral-move machines, and increasing numbers of these alternatives are expected. These systems can achieve considerable labour and water savings, but have significantly higher energy costs associated with water pumping and machine operation. The optimisation of interactions between water, soils, labour, carbon emissions and energy efficiency requires more research and on-farm evaluations. Standardisation of water-use efficiency measures and improved water measurement techniques for surface irrigation are important research outcomes to enable valid irrigation benchmarks to be established and compared. Water-use performance is highly variable between cotton farmers and farming fields and across regions. Therefore, site-specific measurement is important. The range in the presented datasets indicates potential for further improvement in water-use efficiency and productivity on Australian cotton farms.

The Australian cotton industry and governments have funded research into the deep-drainage component of the soil–water balance for several decades. Cotton is dominantly grown in the northern Murray–Darling and Fitzroy Basins, using furrow irrigation on cracking clays. Previously, it was held that furrow irrigation on cracking clays was inherently efficient and there was little deep drainage. This has been shown to be simplistic and generally incorrect. This paper reviews global and northern Australian deep-drainage studies in irrigation, generally at point- or paddock-scale, and the consequences of deep drainage.

For furrow-irrigated fields in Australia, key findings are as follows. (i) Deep drainage varies considerably depending on soil properties and irrigation management, and is not necessarily ‘very small’. Historically, values of 100–250 mm year^–1 were typical, with 3–900 mm year^–1 observed, until water shortage in the 2000s and continued research and extension focussed attention on water-use efficiency (WUE). (ii) More recently, values of 50–100 mm year^–1 have been observed, with no deep drainage in drier years; these levels are lower than global values. (iii) Optimisation (flow rate, field length, cut-off time) of furrow irrigation can at least halve deep drainage. (iv) Cotton is grown on soils with a wide range in texture, sodicity and structure. (v) Deep drainage is moderately to strongly related to total rainfall plus irrigation, as it is globally. (vi) A leaching fraction, to avoid salt build-up in the soil profile, is only needed for irrigation where more saline water is used. Drainage from rainfall often provides an adequate leaching fraction. (vii) Near-saturated conditions occur for at least 2–6 m under irrigated fields, whereas profiles are dry under native vegetation in the same landscapes. (viii) Deep drainage leachate is typically saline and not a source of good quality groundwater recharge. Large losses of nitrate also occur in deep drainage.

The consequences of deep drainage for groundwater and salinity are different where underlying groundwater can be used for pumping (fresh water, high yield; e.g. Condamine alluvia) and where it cannot (saline water or low yield; e.g. Border Rivers alluvia). Continuing improvements in WUE are needed to ensure long-term sustainability of irrigated cropping industries. Globally there is great potential for increased production using existing water supplies, given deep drainage of 10–25% of water delivered to fields and WUE of <50%. Future research priorities are to further characterise water movement through the unsaturated zone and the consequences of deep drainage.

For nearly two decades (1994–2012) a series of three consecutive Cooperative Research Centres (CRC) dealing with cotton production provided the impetus and financial support for a substantial body of soil science research in eastern and northern Australia. Focusing on the most commonly utilised soil for irrigated crop production, the Vertosol, CRC-affiliated soil researchers undertook detailed soil inventories of cotton-growing valleys in New South Wales, and tackled a range of applied soil research questions that faced the entire Australian cotton industry. Across the broad categories of soil mapping and characterisation, soil physical condition, salinity and sodicity, soil chemical fertility, and soil carbon and biota, some 120 CRC-affiliated research papers were published in peer-reviewed journals during the years of the CRC. Findings from this body of research were fed back to the industry through conferences, extension workshops and materials, and to a lesser extent, the peer-reviewed publications. In certain cases, underpinning basic research was carried out concurrently with the more applied research, meaning that the cotton CRC were effectively supporting advances in the discipline of soil science, as well as in sustainable cotton production. A feature of the soil research portfolio over the span of the three cotton CRC was that priorities shifted according to the interplay of three factors; the natural maturation of research topics and the concomitant evolution of cotton farming systems, the rising importance of environmental implications of agricultural land use, and the emergence of carbon as a national research priority. Furthermore, the commitment of the CRC to education resulted in the involvement of undergraduate and postgraduate university students in all aspects of the soil research effort. A legacy of the triumvirate of cotton CRC is a wide-ranging body of both applied and basic knowledge regarding the physical, chemical and biological attributes of Australian Vertosols used for irrigated agriculture.

In the modern era, agriculture must seek to be environmentally sustainable, an obligation now considered as a social contract. This demands that its activities do no significant harm, where the natural resources sustaining it are fully safeguarded, but of necessity in the context of profitable agriculture. The requirement to minimise the environmental impact of the necessary agrochemicals and pesticides in waterways is especially demanding. In the past 20 years, the Australian cotton industry has approached this obligation in various ways, needing extensive planning, learning from past experiences, but it can be legitimately claimed, with significant success. This success has been achieved at some cost, requiring large numbers of personnel, time and resources. This review aims to document the strategies that have been employed, how these required effective research management and how the research data generated was applied. To the extent that this complex program of participatory action has succeeded, while also acknowledging some dramatic failures, other areas of agriculture can also benefit by identification of the key factors contributing to success.

Black root rot is a seedling disease caused by the soil-borne fungal pathogen Thielaviopsis basicola, a species with a worldwide distribution. Diseased plants show blackening of the roots and a reduced number of lateral roots, stunted or slow growth, and delayed flowering or maturity. It was first detected in cotton in Australia in 1989, and by 2004, T. basicola reached all cotton-growing regions in New South Wales and Queensland and the disease was declared as an Australian pandemic. This review covers aspects of the disease that have implications in 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, and crop rotations and host resistance. This review is of special interest to Australian readers; however, the incorporation of ample information on the biology of the pathogen, its interactions with plants and it relation to disease management will benefit readers worldwide.

This article reviews research coordinated by the Australian Cotton Cooperative Research Centre (CRC) that investigated production issues for irrigated cotton at five targeted sites in tropical northern Australia, north of 21°S from Broome in Western Australia to the Burdekin in Queensland. The biotic and abiotic issues for cotton production were investigated with the aim of defining the potential limitations and, where appropriate, building a sustainable technical foundation for a future industry if it were to follow.

Key lessons from the Cotton CRC research effort were: (1) limitations thought to be associated with cotton production in northern Australia can be overcome by developing a deep understanding of biotic and environmental constraints, then tailoring and validating production practices; and (2) transplanting of southern farming practices without consideration of local pest, soil and climatic factors is unlikely to succeed. Two grower guides were published which synthesised the research for new growers into a rational blueprint for sustainable cotton production in each region. In addition to crop production and environmental impact issues, the project identified the following as key elements needed to establish new cropping regions in tropical Australia: rigorous quantification of suitable land and sustainable water yields; support from governments; a long-term funding model for locally based research; the inclusion of traditional owners; and development of human capacity.

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 groundwater levels and changes in groundwater management goals for the Namoi Catchment, which is within the Murray–Darling Basin, Australia. The first high-volume irrigation bore was installed in the cotton-growing districts in the Namoi Catchment in 1966. The development of high-yielding bores made accessible a vast new water supply, enabling cotton growers to buffer the droughts. Prior to the development of a groundwater resource it is difficult to accurately predict how the water at the point of withdrawal is hydraulically connected to recharge zones and nearby surface-water features. This is due to the heterogeneity of the sediments from which the water is withdrawn. It can take years or decades for the impact of groundwater withdrawal to be transmitted kilometres through the aquifer system. We present the analysis of both historical and new groundwater level and streamflow data to quantify the impacts of extensive groundwater withdrawals on the watertable, hydraulic gradients within the semi-confined aquifers, and the movement of water between rivers and aquifers. The results highlight the need to monitor the impacts of irrigated agriculture at both the regional and local scales, and the need for additional research on how to optimise the conjunctive use of both surface-water and groundwater to sustain irrigated agriculture while minimising the impact on groundwater-dependent ecosystems.

Deep drainage under irrigated cotton is not only a waste of a scare resource but also has the potential to cause groundwater levels to rise and cause salinity. Drainage is difficult and expensive to measure directly, so most estimates have relied on modelling or chloride mass-balance calculations. However, direct, accurate measurements of drainage are required to understand drainage processes in cracking clay soils and to provide some certainty about other estimates. A variable-tension lysimeter was installed at 2.1 m depth in a Grey Vertosol under a furrow-irrigated, cotton–wheat rotation. The collection trays were installed without disturbing the overlying soil. A vacuum was applied to the trays and was continuously adjusted to match the matric potential in the surrounding soil at the same depth, thus maintaining the same hydraulic gradient as in the surrounding soil.

The lysimeter was used to measure drainage and other components of the water balance from 2006 to 2011, including three cotton crops, one wheat crop and a long fallow. During this period, two types of drainage were observed. Matrix drainage occurred after an extended period during which rainfall exceeded evapotranspiration. This caused a wetting front to move through the soil over a period of months until it reached the lysimeter and was measured as drainage. Matrix drainage extended over a period of 1 month but at a low rate of ∼0.5 mm/day.

During the cotton season, the earlier irrigations generally caused a sharp peak in drainage of up to 3.5 mm day^–1 ∼25 h after irrigation. However, the water content and soil-water potential at 2.1 m were largely unaffected, and in some cases, the hydraulic gradient was upwards while drainage was occurring. This suggests this drainage is caused by irrigation flowing rapidly through the profile bypassing the soil matrix. Later in the season, when soil-water deficits developed in the subsoil at 0.5–1.0 m between irrigations, the peaks in drainage rate became much smaller.

Bypass drainage appears to account for most of the drainage during the measurement period. Apart from lowering the water use efficiency, it is also more unpredictable and difficult to manage. In addition, bypass drainage is less efficient at removing salt from the soil profile, so that a higher leaching fraction may be required to prevent excessive salt accumulation.

Australian cotton (Gossypium hirsutum L.) is predominantly grown on heavy clay soils (Vertosols). Cotton grown on Vertosols often experiences episodes of low oxygen concentration in the root-zone, particularly after irrigation events. In subsurface drip-irrigation (SDI), cotton receives frequent irrigation and sustained wetting fronts are developed in the rhizosphere. This can lead to poor soil diffusion of oxygen, causing temporal and spatial hypoxia. As cotton is sensitive to waterlogging, exposure to this condition can result in a significant yield penalty. Use of aerated water for drip irrigation (‘oxygation’) can ameliorate hypoxia in the wetting front and, therefore, overcome the negative effects of poor soil aeration. The efficacy of oxygation, delivered via SDI to broadacre cotton, was evaluated over seven seasons (2005–06 to 2012–13). Oxygation of irrigation water by Mazzei air-injector produced significantly (P < 0.001) higher yields (200.3 v. 182.7 g m^–2) and water-use efficiencies. Averaged over seven years, the yield and gross production water-use index of oxygated cotton exceeded that of the control by 10% and 7%, respectively. The improvements in yields and water-use efficiency in response to oxygation could be ascribed to greater root development and increased light interception by the crop canopies, contributing to enhanced crop physiological performance by ameliorating exposure to hypoxia. Oxygation of SDI contributed to improvements in both yields and water-use efficiency, which may contribute to greater economic feasibility of SDI for broadacre cotton production in Vertosols.

Regional climactic variability coupled with an increasing demand on water has placed an even greater pressure on managers to understand the complex relationships between surface water and groundwater in the Murray–Darling Basin. Based on limited soil sampling combined with geophysical observations, past research has suggested that relic subsurface drainage features (also known as palæochannels) have a higher risk of deep drainage and lateral flow, particularly where water is impounded or applied as irrigation. The aim of this study was to investigate the hydrological behaviour of an irrigated 25-ha site in North-western New South Wales in more detail to predict deep drainage risk in the presence of palæochannel systems. Several years of direct and indirect observations, including soil sampling and groundwater measures, were collected. Coupling the field data with one- and two-dimensional water balance models revealed a more complex behaviour where a palæochannel functions like a large underground drain. In contrast to other studies, this study suggests that the actual palæochannel does not pose a higher drainage risk, but the combination of the palæochannels with the surroundings soils does have a higher deep drainage risk.

Groundwater is essential to crop production in many parts of the world, and the provision of clean groundwater is dependent on healthy groundwater ecosystems. To understand better the functioning of groundwater ecosystems, it is necessary to understand how the biota responds to environmental factors, and so distinguish natural variation from human induced changes. This study compares the groundwater biota of the adjacent Gwydir and Namoi River alluvial aquifers, both in the heartland of Australia’s cotton industry, and investigates the relative importance of environmental, anthropogenic, geological, and evolutionary processes on biotic distribution.

Distinct differences in biotic assemblages were recorded between catchments at a community level. However, at a functional level (e.g. microbial activity, stygofauna abundances and richness) both ecosystems were similar. The distribution of biota in both catchments was influenced by similar environmental variables (e.g. geology, carbon availability, season, and land use). Broad trends in biotic distribution were evident: stygofauna responded most strongly to geological variables (reflecting habitat) and microbes to water quality and flow. Agricultural activities influenced biota in both catchments. Although possessing different taxa, the groundwater ecosystems of the two aquifers were functionally similar and responded to similar environmental conditions.

The protection of carbon (C) stores in the form of remnant native vegetation and soils is crucial for minimising C emissions entering the atmosphere. This study estimated C storage in soils, woody vegetation, dead standing vegetation, coarse woody debris, herbaceous vegetation, litter and roots in plant communities commonly encountered on cotton farms. River red gum was the most valuable vegetation type for C storage, having up to 4.5% C content in the surface (0–5 cm) soil, a total-site C store of 216 ± 28 t ha^–1 (mean ± s.e.) and a maximum value of 396.4 t C ha^–1. Grasslands were the least C-dense, with 36.4 ± 3.72 t C ha^–1. The greatest proportion of C in river red gum sites was in standing woody biomass, but in all other vegetation types and especially grasslands, the top 0–30 cm of the soil was the most C-rich component. Aboveground woody vegetation determined total-site C sequestration, as it strongly influenced all other C-storing components, including soil C. This study illustrates the value of native vegetation and the soil beneath for storing large amounts of C. There is a case for rewarding farmers for maintaining and enhancing remnant vegetation to avoid vegetation degradation and loss of existing C stores.