An error from Swansea's Alfie Mawson led to Watford's winning goal at Vicarage Road with defeat leaving the visitors inside the Premier League bottom three.
Etienne Capoue capitalised on Mawson's sloppiness to score the only goal of a dull encounter, the 1-0 win taking Watford onto 40 points and all-but securing their top-flight status.
But it was a fifth loss in six games for the Swans, who are swimming against the tide in their bid to avoid the drop.
Paul Clement's side remained 18th in the table and two points behind Hull, who lost at Stoke, with just five games left to turn their season around.