The 27-year-old suffered anterior cruciate ligament damage during Saturday’s 2-1 home defeat by Blackburn and is facing a lengthy spell on the sidelines.
Manager Jon Whitney told the club’s official website: ‘Joe’s got a long-term knee injury. We’ve had some devastating news this week. It was very innocuous, but it will be long-term.
‘He’s seeing a knee specialist on Friday and we’ll know more after that. He’s definitely out for the season and probably the start of next season as well.
‘All our thoughts are with Joe because it’s a devastating blow for him and for us as a group. The kid is feeling it. We’re thinking it’s an ACL rupture, but we just want it to settle down before we see the specialist.’
Watford boss Javi Gracia does not think Abdoulaye Doucoure's form will be affected by his omission from France's latest squad.