The 26-year-old becomes Phil Brown's first signing since taking over from Paul Sturrock at Roots Hall in March.
White had been at Colchester for 10 years, making over 250 first-team appearances, but rejected a new deal at the end of last season.
He spent a short time on loan at Roots Hall in 2009. White told the club's official website: "I felt now was the right time to move on and I'm pleased that I've been able to join Southend.
"It's a new challenge for me, I've been with Colchester for a very long time, but I can't wait to get stuck into pre-season, get to know the lads and hopefully impress the supporters throughout the season.
"I spoke with the manager and the assistant and the plans they have for the club are exciting and I wanted to be a part of that."
Shrimpers manager Phil Brown added: "John is exactly the type of player we're looking for here at the club for the new season.
"He's a really solid defender who can play anywhere across the back four, but predominantly as a right-back.
"I have had very good recommendations from a number of people including Phil Parkinson (Bradford boss), who said he would have tried to sign him had he been looking for someone in that position."