This has been done for years with wood & canvas, aluminum, fiberglass, and composite canoes and kayaks for years.

Before bringing the boat into the building, Iwould wash the exterior and interior to remove any unwanted palnt or anmimal organisims and chekc to make sure the fibergalass has no breaks.

I would also rinse the boat off with tap water after usage.

Since many pools and bath tubs are make from fibergalss and nylon swimsuits have been used for years in pools, I would not expect there to be any problems for a boat with an intact fiberglass coating. Any bear wood might not fari so good.

More concered with pool contamination from boat. Wash before using in a pool.

Assuming your pool is balanced properly. 

I took my Shearwater Sport Hybrid in. Needed tennis balls on the ends so as not to injure anyone else in the club who might be in the water.

Also took in little Beaker with her Wood Duckling. 

Agree with all the above - really need to have the kit clean to start with. Rinse off chlorine from pool water from any fabric stuff.