Full-back Dunne and centre-half Lowry have completed three-match bans after both were sent off during the 6-0 defeat by Birmingham a fortnight ago.
However, captain Paul Robinson will still be missing from the back four with a thigh injury, although he hopes to be fit to travel to West Ham on Saturday.
Defender Jordan Stewart and on-loan Tottenham youngster Ryan Mason (both groin) are still struggling and midfield duo Therry Racon (ankle) and Tamika Mkandawire (knee) remain long-term absentees.
Jack Smith, Hamer Bouazza and Darius Henderson, who scored his 100th career goal in the FA Cup against Southampton on Saturday, will be facing their former club.
Jonathan Hogg is back in contention for Watford.
The midfielder was absent when the Hornets' FA Cup run ended with a 1-0 defeat to Tottenham on Friday due to a recurrence of a minor knee injury, but is considered fit enough to face the Lions.
New loan signing Alex Kacaniklic is eligible after completing a loan move from Fulham on Tuesday and could be in manager Sean Dyche's squad.
Dyche will still be without defender Martin Taylor (broken toe) and midfielder Stephen McGinn (knee) as the duo are long-term injury absentees.
Watford fans are hoping centre-back Adrian Mariappa and 10-goal striker Marvin Sordell will feature with the January transfer window closing on Tuesday evening.
The pair have both been linked with moves to the Barclays Premier League but Watford insist their star performers will not be sold on the cheap.
Millwall V Watford - view commentary, squad, and statictics of the game live.
Source: PA
