The Vicarage Road outfit have also made an FA Cup semi-final and played some delightful football along the way winning plenty of admirers in the process.
Hornets supporters have never had it so good, yet just as they are getting used to life at the top table, it could all soon come crashing down around them.
Speculation over the future of their charming Spanish manager has been met with incredulity in footballing circles.
But the latest reports emanating from Watford are that Flores is resigned to leaving the club, as reported by the Daily Mail.
Great season has won Hornets plenty of admirers
That's despite Saturday's 3-2 comeback win over Aston Villa propelling his team up to 12th place in the Premier League, level on 44 points with Everton and just three behind champions Chelsea.
I bet if you had asked any Watford fan they would have bitten both hands off for that at the beginning of the season.
But incredibly they could go into next season without the man dubbed the coolest manager in the top flight as owner Gino Pozzo appears certain to invoke a break clause in the summer to end the Spaniard's two-year contract as head coach.
Some would argue Flores was too good for Watford in the first place let alone after having led in such a fantastic return to the top flight.
Be careful what you wish for
Pozzo needs to be careful what he wishes for here. Who will he possibly find better than Flores to take over? Who, after seeing the way Flores has been treated after working wonders, would want to go there?
If indeed Flores' contract is terminated, Pozzo will upset the club's fans and players alike heaping pressure on any new arrival.
Next season's top flight promises to be one of the most fiercely contested in living memory given the riches available for clubs to spend on players.
While the club have stayed up comfortably this season they could quite easily find themselves in the mix for relegation next term.
Make no mistake, Pozzo and the club's delusions of grandeur could come at the highest price.