The widespread adoption of glyphosate tolerant cotton in the last 10 years has substantially modified the weed control practices used in irrigated and dryland cotton crops. Data on changes in the weed populations, infestation levels and flora, and control tactics were compiled from field and industry surveys to compare changes in the weeds and practices used since the introduction of herbicide tolerant cotton. The focus was on three regions: Darling Downs with 36% dryland cotton grown, Gwydir (12%) and Lower Namoi (9%). Across the crop rotations, flaxleaf fleabane had increased dramatically in both dryland and irrigated systems, and there were more residual weeds in dryland than irrigated systems, particularly for bladder ketmia, flaxleaf fleabane, sowthistle and barnyard grass. The main weeds surviving within glyphosate tolerant crops, prior to implementation of remedial actions, were cow vine, flaxleaf fleabane, nut grass, bladder ketmia and barnyard grass, although relative importance differed between the regions. The approach to weed control over the last decade moved from pre-emptive use of residual pre-emergent herbicides to tactics for control of weed seedlings and survivors of glyphosate applications. Weed management practices were similar across the regions but differed somewhat between dryland and irrigated crops. The weed flora shift, threat of glyphosate resistant weeds, and the extent of weeds surviving in the other components of the rotation indicate the need for a more strategic approach to weed management to be applied across the whole cropping system.