We have been in the business of repairing pre-engineered metal buildings since 1996. That’s all we do, pre-engineered metal building repairs. One of the most difficult repairs is replacing an internal gutter. We have a documented the installation procedure for replacing internal gutters to explain why they leak and demonstrate a couple of recent projects.
Below are pictures from a few different buildings. Prior repairs by other contractors were not successful. They tried pouring tar or other products into the gutter and sealed the fasteners on top of the gutter.
Unfortunately for the building owner, that didn’t solve the problems because that’s not why internal gutters leak. Sure, some times they leak at a fastener or one of the gutter seams. However, most of the time water enters the building from under the roof panel.
The roof panels have a “profile” to give the panels strength. The profile includes high ribs. The most common reason internal gutters leak is due to water “splashing”. When the water hits the internal gutter, it splashes, just like a waterfall landing on rocks. When enough of the drops get in it starts to drip. With a heavy rain it may overflow the gutter and the water flow gets heavier.
Below are some pictures we have taken as to what the inside if the high ribs of the panels have looked like
A closure is supposed to be installed. Without a sealant they can get loose. These are 3 ft. long and interlock. 
Sometimes closures aren’t installed at all.
This closure is holding up well 
Often, we will see the insulation folded back. This is very common when a building is newly constructed. New insulation will be effective for a few years before it fails.
Above depicts a roof replacement that includes an internal gutter. We have documented the replacement process below.
First, the roof is cut back to install the internal gutter. 
The internal gutter is laid into place. It is held in place by the frame of the roof.
As the ends are connected, the laps are sealed using three rows of butyl caulk tape and urethane sealant. 
They are stitched together with two rows of fasteners.
Closure is installed at the eave. First, two runs of butyl caulk tape. Then, two runs of closure. The closure is 3’ long and matches the profile of the roof panels. The have a connecting joint, the connecting joints are alternated and provides a backup waterproofing barrier.
Urethane caulk is applied to the top of the closure
The roof panels are secured in place over the top of the closure.
This is what the finished product looks like.
Sometimes an internal gutter is next to a wall. 
The process is the same.
Sometimes we only need to replace the panels at the eave.
Sometimes we replace the entire roof.
The picture above is a standing seam roof with an internal gutter. A standing seam internal gutter replacement is a little more challenging than an R panel screw down roof. There are clips that hold down the panel seams.
Coming soon. We have started replacing the internal gutters in this building. There are 7 internal gutter runs. The building is 1,100 ft. long.