Waters, who takes up the number 9 shirt at The Dunes Hotel Stadium next season, posted on Twitter: "I'd like to say a massive thank you to everyone at Halifax Town.
"I've absolutely loved playing for the club this season and was devastated that we couldn't quite get over the line in the end.
"To the fans, thank you for your incredible support - I hope you can understand my decision to leave.
"To the staff, thank you for giving me the platform to play again and revive my love for the game.
"To the players, thank you for a season to remember. You made every day a joy to come in and I've made friends for life."
Town revealed Waters' departure on Twitter posting: "Waters joined from Torquay United following their play-off heartbreak. The forward went on to make 52 appearances in all competitions, scoring a career best of 20 goals in a single season.
"We wish Bill and his family all the best."
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