You are not going to like this but you need to start looking for where the rust is coming from.
If the source is something like the bottom of the drive gear or the engine oil pan you are going to have trouble with one of them sooner or later.
You also need to figure out how much water is slopping around and figure out how to control it better. There is a point where there is way too much and it will cause damage to something. Just what/when is the question.
May mean doing a better job of packing the rudder and propellor drive shaft stuffing boxes along with more frequent adjustments.
Check for leaks from the drinking water system also.
A small bilge pump in the lowest part of the bilge that can remove almost all of the accumulated water. This pump is not to be confused with the larger capacity emergency centrifugals. Often the much older and maligned Jabsco diaphram water pumps make an effective small quantity dewatering bilge pump as they can be mounted out of the bilge, will pull water up a couple feet, can be fitted with a hose to reach into the deeper parts of the bilge using a small bronze screen on the hose end. Even a used but running pressure water pump can be fitted with the bilge pumping valves which have larger holes to pass more garbage with monkeying the valves.
A standard type of centrifugal pump may not be good enough for that purpose as they will leave a lot of water they simply cannot evacuate.
To me the most likely sources of rust are the engine/gear box, steel tanks whether fuel or water, steering gear supports such as the main anchor for the steer cylinder, generator, water maker , and so on. I don't know what you have but start sorting it out.
If you are lucky maybe it is just an old lost in the bilge piece of forgotten steel or steel equipment. But find out.
Empty all the gear in the bilges and look seriously. If need be get one , or borrow one, of the remote cameras with the flexible heads. They have come down a lot in price over the last few years.
