Nugent and selector Michael Monaghan made their announcements after the Munster champions were crushed by Kerry in the provincial semi-final on Wednesday night.
“There are major problems with the football structures in this county,” a bitterly disappointed Nugent said.
“It is like trying to keep the tide out. There is no point in trying to conceal that and right now morale among the football people of Waterford is at rock bottom,” he said.
“I didn’t think things would end this way, but having trained so hard since last January, both inside and outside the gym I don’t believe that we have been fairly treated.”
Nugent had been angered by the late withdrawal of county senior hurling panelist Michael Walsh and Shane Walsh who was injured in a divisional final which the west board refused to postpone.
Walsh insisted that his withdrawal was because of his injury, but Nugent is convinced that it was on the “recommendation’ of the county senior hurling selectors that he opted out.
One of those selectors, Seamie Hannon, repeated yesterday that Walsh is injured and is continuing to receive treatment as Waterford’s preparations continue for Sunday week’s All-Ireland semi-final.
The one year term of the county senior football manager, Billy Harty, is also at an end and it is unlikely that he will be seeking another term.
With the departure of Pat Nugent two top posts are vacant and no one immediately identifiable to fill them.