Two second-half goals from the visitors earn them three points at the JobServe Community Stadium in a difficult afternoon for the U's.
After a goalless first half, Tom Dallison netted the opener, an own goal in front of the travelling away fans to put Barrow a goal ahead. And Josh Kay put the icing on the cake for the Bluebirds with a nintieth minute goal to seal the victory.
Hayden Mullins named a side with three changes to the side that was defeated 2-0 at Forest Green Rovers in the week, with Tommy Smith, Noah Chilvers and Tom Eastman all dropped to the bench.
Coming in to take their places were Miles Welch-Hayes, Freddie Sears and Tom Dallison in the starting eleven, with newest signing, Emyr Huws named on the bench alongside Frank Nouble after recovering from injury.
The opening half hour of the game presented chances to both sides, but both lacked that little bit of quality that would have seen them take the lead.
Freddie Sears tested Paul Farman with an effort from just outside the area with an early shot after just three minutes, but the Barrow 'keeper was always equal to it, not having to stray far from the centre of his goal.
The visitors had a good couple of chances, after earning succession of corners mid-way through the first period, with Brough and Wakeling having efforts on goal. Brough's came after Turner had punched the ball clear, with the centre-half strikign the ball straight back into a crowded area, where it was deflected over.
And Wakeling went close from the resulting corner. Getting his head to the ball and flicking it across goal, the Leicester loanee saw his effort fly just past the post and out for a goal kick to the U's.
The best chance of the game so far presented itself to Miles Welch-Hayes, who was returning to the side for the first time since November, with the defender heading just wide. Cam Coxe did well to beat Remeao to the byline an deilver a cross, with Brendan Wiredu flicking the ball on. But Welch-Hayes wasn't able to divert the ball into the net at the back post with the goal gaping, and it would remain goalless until the break.
But after half time, it was the visitors who took the lead in unfortunate circumstances for the U's. Luke James delivered a low, pacey ball into the area, with Tom Dallison slicing his clearance into his own goal, in front of the celebrating away fans.
Both Freddie Sears and Corie Andrews went close to levelling the scores just after the visitors' breakthrough, with Sears seeing his effort stopped by the outstretched leg of Paul Farman. But Andrews had a perhaps easier chance, failing to convert at the back post from Tchamadeu's deep cross, with the near post unguarded.
But the U's were unable to get level, with Mark Cooper's Barrow side adding a second with the game entering injury time. Josh Kay was the man on target, with a low drive at the near post that deflected in off Jake Turner.
The U's remain in twenty-second after the defeat, facing a trip to fifth-placed Sutton United in the next game, on Tuesday evening.
Colchester United starting XI: Turner, Welch-Hayes (Hannant 58'), Chambers, Wiredu (Chilvers 63'), Skuse, Judge, Sears, Dallison, Andrews (Nouble 82'), Tchamadeu, Coxe.
Unused subs: Gerken, Smith, Eastman, Huws.
Barrow starting XI: Farman, Brough, Platt, White, Jones, Harris (Devitt 76'), Glennon, Wakeling (Kay 63'), Hutton, Banks, James.
Unused subs: Lillis, Brown, Ellis, Devitt, Stevens.