Ahh, Houston is about 50' msl or so (and slowly sinking as the aquifers are depleted - they don't re-inflate much). Considering all of the tunnels downtown, I'm sure there is an extensive sump system.
The Texas Medical Center learned a hard lesson with Allison in 2001...
There are four major not for profit/teaching hospitals located in a row, plus one of two medical schools in the line. Every single one of them - Memorial Hermann, UT Health Science Center at Houston, Houston Methodist, St Lukes and Texas Childrens, plus a shared physical plant, were all connected on the basement level by passageways large enough to drive through.
Once the water began to flood one, they all were flooded, sidelining major portions of the hospitals for months.
Now they all have massive submarine doors at multiple points to contain flooding, as well as all mission critical switchgear and generators being up out of harms way, as well as sumps/pumps.
Everybody has a flood plan that activates when the water level in a particular box culvert rises above a certain level (a former creek taken underground, that runs from Rice University, near Hermann, Ben Taub and thence into Brae's Bayou near Cambridge and Holcome blvd. If you look on Google Maps you can see the culvert dump into the bayou). If it gets high enough, they button up the submarine doors.
Cant speak to the downtown tunnel system, but given that they are all privately owned by the various buildings they pass under, I would suspect that each property owner would have their own doors and protocol.