The 29-year-old has missed practice this week due to a hamstring strain while he also sat out his side's season-opening win against the Carolina Panthers.
Carroll told reporters: "He's doubtful going into the game. We'll see what happens on game day. We'll take it all the way up until then – has not been able to get as much work as we'd hoped.
"Just wasn't right enough. He's still working and running in rehab but we did not get him on the field."
Seattle split their games with the 49ers last season as they finished second in the NFC West.