After Hurricane Sandy, it took almost a week to reopen the subway tunnels.
I can just imagine the kind of kinetic force that'll occur if a sled carrying a car slams into a section that has a few feet of water.
Airflow and humidity are other concerns. Airflow is necessary to keep passengers safe. Controlling humidity is important for keeping the infrastructure from degrading more quickly.
Any good paints or fabrics or metamaterials that could be used as a tunnel liner that only allow water to wick in one direction (from tunnel internals to surrounding soil)?