There have been rumblings of discontent behind the scenes for some while and it appeared that Waggott was not popular with the Valley staff.
It always seemed strange that his predecessor, Peter Varney, was entrusted with looking for new investment while Varney's former assistant, Steve Sutherland, dealt with sponsorship. Even after Sutherland himself left, he sourced the new kit deal with Macron.
Following Varney was always going to be a tough job and it seemed to be too big an ask for Waggott.
Steve, a native Geordie, was a talented schoolboy footballer who trained as a PE teacher and has also worked as a sports journalist and agent.
He first worked for the club's community trust before succeeding Varney two years ago. He will continue to assist Murray during the transfer window.
Murray paid him this tribute:'Steve, the board of directors and I have agreed that Steve will leave his role as CEO at the end of the month, but he will continue to assist me during the transfer window on reshaping the first-team squad for the forthcoming season.
'All the directors and I would like to thank Steve for all his hard work over the past two difficult years, and we wish him well in the future."
Waggott responded:'It has been a real honour and privilege to work at Charlton over the past six and a half years, as chief executive of first the Charlton Community Trust and then the football club.
'Given the financial climate and two relegations in four seasons, it has been a difficult role to fulfil over the past two years, and we were all hoping that the club would get back to Championship status at the first attempt, which would have secured vital additional income.
'This didn't happen, and therefore in the current circumstances the club must restructure at all levels, including the executive level - so, following a series of discussions and meetings, a decision was taken by the board for me to leave.
'Charlton is a great club, with loyal supporters and true community and family values, and I hope the club bounces back next season, returning to the Championship and progressing from there.
'I would like to thank all the staff for their tremendous input and hard work while I've been chief executive.'
Managing Director, Steven Kavanagh, will oversee the day-to-day activities at the Valley from the beginning of July.