Although the LHC is running through the territory of a few municipalities, only one
of them had as much as three floodings between 1983 and 2004, the remaining ones
even less than three [38]. As there have been no reported consequences for the LHC
tunnel, a natural cause for flooding will not be the crucial factor for the determination
of the probability of occurrence.
Climate change might change that but it doesn't seem like long term flooding is a major risk even if abandoned.
Flooding would be catastrophic even today, but it is not uncommon for rainwater and groundwater to fill spaces over time. Most abandoned US missile solos are filled because of rain and it is not uncommon for old, abandoned bunkers to be filled too. If we're comparing it to an "ancient" structure it can add up.
The LHC currently uses sump pumps to deal with natural water infiltration. Without those pumps the water can collect in the space. There are also installed sources of water that could leak over time, such as for firefighting.