Installing a shotcrete lining requires a somewhat dry substrate and certainly is not compatible with running water. The water needs to be blocked or diverted.
A means of blocking the inflow is to inject a swellable urethane grout through the openings in the existing pipe. The grout, if done properly, will expand upon contact with water and seal the outside of the pipe. Another means of diverting the water is to install drainage material over the inflowing area to collect the water and remove it from the pipe. The shotcrete can then be applied over the drainage material.