I have a 1993 powerquest 257 with a 502 efi. Something strange is going on with my charging system. Initially I was thinking either battery, alternator, or voltage regulator. Had all three checked out and everything is great with them. I did some digging and found a loose wire on back of main breaker on engine by ECM. I was very thankful I found it and thought problem was fixed. I ran the boat on hose out of water and had 14.7 volts. Everything looking great so I ran her on the water this past weekend. What is strange is when I am in the water, I am only reading around 13.7 volts with nothing on (cabin lights, blower, etc.). It will run at around 13.7 volts for a period of time, then randomly drops down to 12 which ofcourse makes me nervous. It will ran at 12 volts for a bit then back up to around 13 she goes. I am stumped and the only thing I can come up with is it only happens when in the water, which tells me it is something electrical on the back
On back of transom. Is it possible for the mercathode system to cause this drain? Or possibly trim sender or trim switch? Any replies are greatly appreciated!!

Are the voltages you are giving while the engine is running? If so, it's not the Mercathode system, it can't pull that kind of power without toasting itself. If not, it's a possibility, but easy to test- disconnect it and see if the voltages stabilize.

Trim sender & switch can be testedd the same way, but are less likely culprits IMO.

Yes the engine is running while I check the voltage in both cases (on the water and off). How could I check the trim sender on the water?

get another volt gauge and run separate wires to the battery and see what happens. I have seen dozens of volt meters in the dash that showed 10 or 11 volts but the battery was seeing 14. bad or weak grounds at the dash or old gauges can show odd things.

Trim sender & switch are connected with bullet connectors inside the boat, so they can be disconnected while on the water.

Compedgemarine's advice above is good - I assumed you were using a handheld voltmeter. If not, get one - dash guages are not reliable, and should be verified before trying to solve a problem.

I was thinking the same so I did in fact use a handheld volt meter. I forgot to mention that when I ran at night, with my nav and stern lights on, I would actually see the lights dim when the voltage would randomly drop. I don't put much faith in my meter on the dash but it still gives me a ballpark figure when the drop happens.

If your alternator is good and you have 2 batteries and you drop from 13.7 to 12 volts, that would take a significant amount of current to cause, probably more than 20 amps. It sounds more like a bad ground on the motor or loose wire in the charging circuit. Either that or the regulator is not consistent.

I am only running one battery. I am thinking the same about the regulator not being consistent. I checked every wire in the charging circuit when I initially found a loose one on back of breaker. I also checked the grounds. I plan on taking out for a run this week to see how it acts and do more troubleshooting on the water.