Argyle captain Karl Duguid's classy finish on the half-hour mark was added to by Luke Summerfield's 72nd-minute penalty after Hornets captain Jay DeMerit had inexplicably handled.
John-Joe O'Toole scored a late goal for the third home game in a ro
w but it was not enough for Boothroyd's side.
And after seeing both striker Tamas Priskin and right-back Lloyd Doyley carried off with hamstring injuries, Boothroyd admitted that his threadbare squad is stretched beyond its limits.
He said: "If you were to say we are in for a long, hard winter I would have to get my coat and agree with you.
"We've got one recognised centre-forward at the club.
"With our best 11 players on the pitch we'll go toe-to-toe with anyone but to lose two players with hamstring injuries is a massive blow.
"Plymouth made seven changes but if I made seven changes I would have had the physio at right-back.
"I'm going to have a chat with the chairman and see what's available because it's a lot to ask for this squad to play as many games as we have got coming up."
Argyle climbed off the foot of the Coca-Cola Championship table with the three points but Boothroyd believed his side gave their all.
