I am very worried after reading these comments in today's (10 April 2019):
http://ottawacitizen.com/opinion/letters/todays-letters-the-leaky-tunnel-and-other-lrt-problems-in-ottawa

I don't have much knowledge about this issue, and that what worries me. Is the tunnel safe?

Will the waterprooffing issue come back to haunt us?

I also have a spinoff question that is mainly technical. In case the tunnel would have to be closed because of issues like flooding, would OCTranspo run trains between Blair and uOttawa?

1 hour ago, Phil said:

I don't have much knowledge about this issue, and that what worries me. Is the tunnel safe?

Like every other component of the line, the tunnel needs to satisfy the City's requirements (which includes safety) before they'll accept a handover. 

Tunnels leaking is very common and can be mitigated. The Dow's Lake tunnel that the Trillium Line uses leaks (there's a pump building in the Arboretum), and just as another example would be the pedestrian tunnels at Carleton University. As long as the tunnel is regularly inspected (which it will be) for water damage, and as long as the pumping system (and backup system) stays intact, the tunnel will be fine. If there were any kind of flooding severe enough to flood the tunnel beyond use, then the city as a whole would be shut down.

1 hour ago, Phil said:

I also have a spinoff question that is mainly technical. In case the tunnel would have to be closed because of issues like flooding, would OCTranspo run trains between Blair and uOttawa?

It's possible. They have the crossover track just before the tunnel, so they would be able to turn trains around.

I too would not be concerned. Water infiltration, while unfortunate is a fact of nature. This happens everywhere, whether the tunnel passes under a waterway, or under solid ground. Water will find the weakest point, a small crack, a fracture, a hairline split and come through. Over time, the water will expand the opening and it will increase.

All cities have mitigation measures in place, to help manage and contain the flow of the water.

For example, Montreal's Metro stations all have some level of water infiltration. If you are observant, you will see conduits that have been added to the tunnel and station ceilings where water has entered, to help reroute the water away towards proper drainage. Also in Montreal ,on the guideway and below the tracks, you can see puddles or water on the ground, despite the fact that the metro vehicles never go outdoors, all is contained indoors.

On 4/10/2019 at 2:11 PM, Phil said:

I also have a spinoff question that is mainly technical. In case the tunnel would have to be closed because of issues like flooding, would OCTranspo run trains between Blair and uOttawa?

Idk about going to uOttawa, since at the end of the line they'd need to have a place for people to transfer onto buses from. So they might only go as far west as Hurdman, since that has the space for the amount of buses needed. They might deem it to confusing for the general public if they have people transfer onto the buses at Hurdman to go deep downtown, or more west when there's still a line going into a part of downtown.

As the initial line is not extremely long, the options are fairly limited for offering a reduced service, however once Stage 2 is up and running I'm sure there will be quite a few scenarios that they could work with if certain sections are not available or need to be closed.

For the Stage 1, I would expect Tunney's to uOttawa, and Blair to Parliament, based on what would make sense from seeing the track switches and crossovers. Of course other scenarios are possible but the the line segments become quite short, and running a train to move people only three stations makes less sense.

From the city's presentation that "It wouldn't be pretty" if the line closed, I am sure that they would try to operate if it still made sense to, despite a closure. As is done in other cities, if a station needs to be closed, and the incident doesn't involve the track or guideway, the trains could simply not stop and bypass it and go to the next instead.

Overall, I am sure they will do whatever they can to keep it running, in whatever form, should there be an incident.