Salby was the first to document the influence of meteorological variability on long-term stratospheric ozone changes. This role of natural variability on stratospheric ozone depletion has inspired related studies and large research projects and has been recognised in several WMOOzone Depletion Assessments.
In 1994 Salby set up a non-profit company to receive federal award funds from the National Science Foundation and other agencies for research in parallel with his research work at the University of Colorado, and in 2003 he formed another company as a subcontractor to receive charges for his efforts. Following allegations of an overlap between funding applications, the National Science Foundation began an investigation in March 2005. It advised the University of Colorado, which sought information from Salby but he did not cooperate with this investigation. In October 2006 the university produced its investigation memo, and suspended Salby's privilege of submitting proposals from the university as well as restricting his access to university research facilities. In 2007, Salby was on sabbatical in Australia. Before the university made its final adjudication, Salby resigned from his faculty position. The National Science Foundation investigation report issued on 20 February 2009 found that Salby had overcharged his grants and violated financial conflict of interest policies, displaying "a pattern of deception, a lack of integrity, and a persistent and intentional disregard of NSF and University rules and policies" and a "consistent willingness to violate rules and regulations, whether federal or local, for his personal benefit." It debarred Salby from receiving federal assistance and benefits until 13 August 2012.
After leaving Colorado, Salby joined the faculty of Macquarie University in Australia, where he was appointed Professor of Climate Risk in 2008. In May 2011, Salby's research showing that ozone levels over Antarctica had begun to recover since the Montreal Protocol banned the use of ozone-depleting substances, was published in Geophysical Research Letters. Macquarie terminated Salby's employment in 2013 after an extended period during which he repeatedly refused to fulfil his teaching responsibilities, and ultimately failed to turn up to take a scheduled class. Salby also ignored written instructions, made an unauthorised trip to Europe, and inappropriately used university resources including a corporate credit card. When this was discovered, the university cancelled his return ticket from Paris. Macquarie University stated that the dismissal was due to Salby's misconduct, and not "in any way related to his views on climate science". In Salby v Macquarie University Justice Rolf Driver of the Federal Circuit Court of Australia ruled that Salby had failed to establish any of the elements of his case against Macquarie University regarding the termination of his employment and dismissed the case. Salby published a counterstatement.