The 30-year-old, who joined the club on a free transfer in 2009, will depart having made 133 appearances for the League Two outfit.
"It's a similar story to Nick Fenton really. We wanted to keep Will and he wanted to stay but we could only offer reduced terms and couldn't agree a deal to keep him here at this moment in time," Bentley told the club's official website.
"It's another disappointment for us as he showed [against Southend] just what a good player he is but we know what we have to work with next season and that has to be the way forward.
"I would like to thank Will for everything he has done for us. He has been a great lad to have around and we wish him well for the future."
Morecambe finished the League Two season in 16th position.