The ground level of those buildings are used for storing the boats and racing shells, and yeah, they do get flooded. I rather suspect water creeps into the boathouses most years.
This is the 2006 flood, a day or two before the Schuylkill River crested. It's not at all uncommon for the Schuylkill to rise over its banks every year ... if not several times a year. Most of those times it's mild flooding along this part of the river where it's wide. However, just about any time it rains, we have flash flood warnings.
In 2014, the river crested higher than it did during Hurricane Irene and Superstorm Sandy. 2011 was another really bad flood year. That storm not only closed the roads on both sides of the river, but the Schuylkill Expressway (my alternate route when MLK Jr Drive is flooded) was also closed because of a mudslide.
This next picture is just past Boathouse Row on the other side of the spillway. That's the Fairmount Water Works which provided water to Philadelphia until 1909. The huge brownish building behind the Water Works is the Museum.
This is what the Schuylkill River has looked like most of the summer since we've had so little rain. Though, it's even gotten lower with a lot more of the rock shelves exposed. The picture of Boathouse Row with the duckweed was after a day of rain. After heavy storms, the downside of the spillway is level with the upside.
Inside one of the boathouses after the river came to visit in 2010.