The inside of the tunnel isn't in anybody's waters, and the two nations have established an agreement on such matters, the Protocol concerning frontier controls and policing, cooperation in criminal justice, public safety and mutual assistance relating to the Channel fixed link. It provides for each state to exercise jurisdiction in "control zones" on each other's territory (e.g. border control areas). The frontier itself is set at the mid-point of the tunnel by the Treaty of Canterbury (the 1986 one, the 1416 was about an alliance against France).
Within the tunnel itself, Article 38 of the Protocol says that each state has jurisdiction on its territory, including the parts of the tunnels on their side of the border, but provides for either state to have jurisdiction in a number of cases, such as where nobody is sure where an offense happened, and gives priority to whichever state catches someone first.
The frontier is marked inside the service tunnel.
As for the waters above the tunnel, this map indicates the narrow area of the Strait of Dover lies entirely within either UK or French territorial waters.