With a massive FA Cup quarter-final to come on Monday night, Clarke opted to make nine changes to his side, prioritising the FA Cup now that Reading's safety is all but assured.
Goals from Almen Abdi, Matej Vydra, Troy Deeney and Forestieri gave Watford victory in a one-sided contest, whilst Jem Karacan gave Reading fans something to cheer as he netted his first goal since a 16-month lay-off.
The defeat leaves Reading 17th in the Championship, 10 points above the drop zone after Wigan won at Rotherham.
Clarke made nine changes in total as Jure Travner and Zat Knight were handed their debuts, whilst Niall Keown and Jack Stacey made their first league start.
Mikkel Andersen, Danny Guthrie, Jake Taylor, Simon Cox and Yakubu also came in, as only Hope Akpan and Jake Cooper kept their place in the team from Brighton.
Reading lined up in a 3-5-2 formation but their back three of Knight, Cooper and Keown was instantly breached as Watford took the lead within 52 seconds.
A spell of Watford pressure ended with Troy Deeney finding Abdi on the edge of the box and his instinctive effort with the outside of the foot found the bottom left-hand corner as the hosts seized the initiative early on.
It proved to be Abdi's only contribution as the Watford man was forced off through injury just five minutes later – but his replacement was arguably the best player on the pitch for the remaining 83 minutes.
Fernando Forestieri ran Reading ragged and set up two goals as well as going close with numerous efforts on Andersen's goal.
It was close to being 2-0 in the ninth minute when Marco Motta's dipping volley from 30 yards crashed off the crossbar but Reading survived the melee that followed.
Clarke's side had glimpses of openings against a nervous Watford defence but they couldn't take advantage and had just a couple of Yakubu efforts from distance to show for their efforts.
Watford were cutting Reading apart at ease and only a superb reflex save from Andersen stopped Forestieri's acrobatic volley doubling their lead in the 29th minute.
It was a brief let-off though as the hosts' constant pressure eventually told in the 40th minute when Vydra beat Andersen at his near post.
Forestieri was again key as his jinking run saw him create a gap to be able to slip the ball to Vydra, who fired high past Andersen to set Watford on their way to a routine victory.
It was a deserved half-time lead for Watford and Reading were struggling to live with the movement and attacking prowess of the hosts.
Clarke's side had started the first half poorly and it was a similar story in the second half – this time it took 170 seconds for Watford to strike.
Forestieri beat Knight and got to the byline, squaring for Deeney to tap into an empty net from a yard out.
The 1,008 Reading fans behind the goal would've been fearing the worst at this point but the Royals dug in.
With all three points assured for Watford and the Royals keen to avoid a heavy hammering, the game had the sense of a pre-season friendly about it, until Karacan and Nick Blackman were introduced.
Karacan was given a massive reception by the Reading fans and he thanked them for it in style, curling home from 25 yards following a corner that wasn't cleared properly.
It was a great moment for the Royals skipper and the goal gave Reading fresh impetus as they threatened to stage an unlikely comeback.
Yakubu and Blackman tested Heurelho Gomes in the aftermath of the equaliser but it was short-lived as Forestieri struck in the 85th minute to seal victory.
The creative midfielder had set up Deeney for his third and it was roles reversed for the fourth goal as Deeney sent Forestieri clear of the Reading defence and he fired across Andersen to complete the scoring.
Reading Mikkel Andersen; Niall Keown, Zat Knight (Andrija Novakovich '85). , Jake Cooper, Jure Travner; Jake Taylor (Jem Karacan '59), Hope Akpan, Danny Guthrie, Jack Stacey; Simon Cox (Nick Blackman '59), Yakubu. Subs: Dan Lincoln, Sean Long, Aaron Kuhl, Ryan Edwards,
WatfordHeurelho Gomes; Marco Motta, Joel Ekstrand, CraigCathcart, Daniel Pudil, Ben Watson, Adlene Guedioura, Daniel Tozser, Almen Abdi(FernandoMatej Vydra, Troy Deeney. Subs: Jonathan Bond, Miguel Layun, Fernando Forestieri, Lloyd Doyley, Juan Carlos Paredes, Ikechi Anya, Gabriele Angela
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