So first of all, just to be clear, that would count as a constrained or confined flow, so Betz's law wouldn't apply.
As for the details of the flow, either the depth after the turbines is higher, thus providing a larger cross section and slower flow, or there's a drop in water level across the turbines and thus the energy extraction comes from gravitational potential energy. One or the other must be true though - you can't extract energy from a flow and also have the outlet flow with the same velocity, cross section, and water level as the inlet.
EDIT: If it were fully confined to a pipe (which is not the case above, but I just want to cover all the scenarios here), you could have both the inlet and outlet with the same velocity and cross sectional area and nevertheless extract energy. In that case though, you'd see a pressure drop across the energy extracting turbine. For the generalized case, you'll always see a drop in gravitational potential, pressure, or velocity if you extract energy from a fluid.