This study was undertaken to identify factors in Australian cotton farming systems that influence yield and fibre quality of cotton and how these have changed with time after the wide adoption of Bollgard II^® cultivars (containing the proteins Cry1Ac and Cry2Ab, providing easier control of Helicoverpa spp.) in the 2003–04 season. Data from Australian commercial cotton variety trials conducted from 2004 to 2011 were used to link management inputs, yield, and fibre quality.

Restricted (residual) maximum likelihood (REML) and regression analyses were used to determine which factors had a significant effect on yield and fibre quality. Results showed that lint yield was significantly influenced by cultivar and growing region, and the interaction between region and the amount of applied nitrogen and phosphorus (kg ha^–1), plant stand (plants ha^–1), in-crop rainfall (mm) and the number of irrigations, season length (days), and days to defoliation. Generally, the same factors also influenced fibre quality. Regression analysis captured 41, 71, 50, 30, and 36% of the variability in lint yield, fibre length, micronaire, fibre strength, and trash, respectively, for irrigated systems. For dryland systems the variability captured was 97, 87, 77 80, and 78%, respectively.

Changes in cotton farming systems from 2004 to 2011 have occurred with applied nitrogen fertiliser increasing under irrigation and decreasing under dryland systems. However, phosphorus fertiliser use has remained steady under irrigated and decreased under dryland systems, and the number of insect sprayings has decreased under both systems. Under irrigated systems, lint yield, fibre length, and trash levels increased while micronaire and fibre strength decreased. Under dryland systems, lint yield decreased while micronaire, fibre length, strength, and trash levels increased. All fibre quality parameters satisfied criteria that would not incur a penalty.

The results considering which factors are the most important and which are of lesser importance provide some insight to changes in management in both irrigated and dryland systems and the effect on lint yield and fibre quality and provide some basis for future investment in research and development and extension to the Australian cotton industry.