Hi narrow_boat_uk
Welcome to the forum
Normally the only place water gets in is through the stern tube stuffing box or deep sea seal, whichever is fitted. It is possible the water has come from an internal leak from the fresh water tank or pipework, or simply rain water due to a hatch being left open. In a hull that has seen some life a bit of rust is to be expected, but if it is deep flaked rust and not just surface rust, e.g. if it leaves deep indentations 1mm or more when removed, you might consider getting an ultrasound check done the next time she is pulled out to determine the hull thickness. Most hulls are 6mm sides and thicker for the base plate, this can vary but not usually by much, and it takes a long time to rust through 6mm.