Flores' position as head coach is apparently under threat despite what, on the face of it, appears to have been a hugely successful campaign.
The promoted Hornets have secured Barclays Premier League safety with room to spare and on Sunday tackle Crystal Palace in an FA Cup semi-final.
Yet owner Gino Pozzo, who got through four bosses last season, is believed to be considering another change following a run of just three league wins since the turn of the year.
Former Tottenham midfielder Capoue feels the Spaniard will take Watford further forward if he is given the opportunity to do so
The 27-year-old said: "Can the team improve? Of course, because it's our first season
We are a new team in the Premier League.
"We expected to have a good year but we have had a very good one with a lot of new players.
"Now he knows everyone and new players will come in next season to reach another step in the Premier League, so why not?
"(His future) is none of my business, I just do my job
But he has had a very good season and he's a good manager."
Capoue, frozen out at White Hart Lane until leaving for Watford last summer, has enjoyed a new lease of life under Flores having formed a close bond with the former Valencia boss.
"We have a special relationship," he added
"It's more human than just talking about football.
"That's what helped to push me on
He's a human being and understands me and I understand him
It's a simple relationship.
"We talk about anything outside football
We try to know each other and what we like
It's like a dad and son, or a big brother and small brother
We have the same relationship."
France international Capoue is hoping to make it third time lucky against the Eagles at Wembley after experiencing two unsuccessful semi-finals while paying for Toulouse.
"It's my third semi-final after two in France
I lost twice so I hope the third isn't the same," he said.
"I played in the national team in a tough qualifier, but this is one of the most important games of my career."
Source : PA
Source: PA