The Hornets announced earlier this week that they will part company with Mazzarri at the end of this season, with the club having lost their last five matches to slump down to 16th in the Premier League table.
The Italian's decision to leave Deeney out of his starting lineup at various stages of the campaign is thought to have put a strain on the relationship between the pair, but Mazzarri insists that he has been happy with his skipper's contribution.
"I want to speak about the facts. Deeney is a player who scored more than last year, he played a lot this year and he helped the team reach the 40 points. This is what counts for me, nothing else," he told reporters.
"My choices this season have always been for the best of my team. When he was out it was because there was a decision [to be made]. I knew why he had to go out. I want to thank him again and the players for giving 200%."
Mazzarri's last match in charge of Watford will come against Manchester City on Sunday.