The long-serving defender was stretchered off after 50 minutes of the club's goalless draw at bottom club Southampton with knee and ankle problems.
Baldwin landed awkwardly while defending a corner and faces a spell on the sidelines.
"I went up for a header and I landed awkwardly on my ankle," he told the Colchester Gazette. "Then one of their players landed on my leg.
"It's frustrating but it's not the first time that something like this has happened in my career.
"I hope to be back as soon as possible and fingers crossed it's not too bad."