I am a fairly good mechanic but I have never worked on an outboard motor before. I am trying to decide whether or not to try and do the work myself or have it done. It is a 2006 it had 2 years of running in a river with tide water so some salt water only about 40 hours total. the third year it just sat. It was not flushed out properly so I am assuming that the water pump or the thermostat are all coroded. What do you think?

Ok I dug into it a little and I found the thermostat and changed it out that was real easy. The Pee hole was plugged and I cleared that and it is pumping water now. But it is still overheating. I am using the ear muffs to supply water and some say that is not enough. Is that the reason it is overheating. I hate to dig into the water pump if it is ok. If it is pushing water out the pee hole does that mean that the water pump is ok?

If you've never changed the impeller then I would do that. It's not that bad of a job, but you didn't say what motor you have.

BF40 Honda outboard.
Is it under the flywheel?

It's in the lower unit.