The 33-year-old has spent the last five years at Vicarage Road, with his only break coming during a loan spell at Derby County in 2009.
He remains the Hornets' club captain, but struggled for action in 2012/13 as Gianfranco Zola put his side in promotion contention.
Watford are keen for Eustace to stay on at the club, possibly in a coaching role, but he is not ready to hang up his boots just yet.
Eustace's representative Colin Gordon said in the Watford Observer: "Watford wanted John to stay with the club in some capacity, but John wants to continue playing.
"Gianfranco Zola really likes him as a bloke and really wanted him to stay around the place and everyone who knows John knows he will make a top manager one day.
"But he wants to continue playing - he wanted assurances about playing time and things like that and Watford couldn't give him that.
"It's disappointing we couldn't come to an agreement and that it's petered out in this way, but the club have been very fair with us and we part on good terms."