Mercury 40hp 4 stroke overheating

I have a 1999 Mercury 40hp 4 stroke tiller that has a warning signal going off. It started last season when I back trolled. I could only back troll a few minutes before the warning signal would go off. Before my trip to Rainy River this spring I took it into the dealer with the plan of having my impeller replaced. Their tech said it was a oil sensor causing the alarm to go off so they changed that. Well that didn’t solve the problem and it only got worse as the trip went on. It didn’t matter if I was going forward or reverse the warning would go off. After the trip I took it back to the dealer and had the water impeller replaced. Next trip out I idled out past the no wake zone opened it up and 5 seconds later same deal. I checked the thermostat this afternoon and it operated like it’s suppose to. I flushed it out this afternoon after this I’m at a loss. Anyone have any ideas on what I could check next?

something you may want to try,sometimes the computer holds a code in memory and wont clear itself once the problem is fixed,so unhook your engines battery overnight.
this will allow the small capacitors that act like batteries to die out and the ECM will reset itself.

next morning reconnect your battery and give it a go,if the alarm returns,you are either low on oil pressure in the engine itself,or the temperature sensor is bad.

Have you confirmed that it actually is overheating or is it just the alarm going off that gets annoying?

Is it the oil alarm or the overheat alarm? One is a constant beep, the other is a beep, beep, beep (can’t recall which is which). I’ve had both sensors go out in the past, but when they’ve gone out, they’d start again as soon as the key is turned on.

I know it was overheating after the oil sensor was replaced. When the warning signal went off after the impeller was replaced I shut it off and used my trolling motors to fish and get me back to the ramp. I was to PO’d to do any diagnostics.

The warning signal is one continuous beep.

I’ll try disconnecting the battery and see where that gets me.

Thanks for the replys.

if you are sure its the overheat alarm,and disconnecting the battery does not clear it and it returns,try disconnecting the temp sensor,if the alarm quits then and you are positive it is not heating up,the sensor may be bad and needs replaced.

they are not terribly expensive,and are easy to replace.

Good info iowaboy, thanks!

Still goes back to my original question, is the motor actually overheating or is it just an alarm?

Steve O,
I have a similar motor on my pontoon. Mine is a 2000 40 hp 4 stroke. Unfortunately, I’ve had a similar issue you are having and still have it. I took mine to Crystal Pierz (Rice Lake) 3 or 4 times over 2 years and they were never able to fix it. I probably spent over a 1000.00 (impellor twice and some other things I don’t recall). I would pick it up and put it in the lake and the SOB alarm would beep within 10 minutes. I then started taking it to Roberts Marine. I think I had it there 2 times. Same results. They would run it in a tank for hours and not able to get the alarm to trip. I gave up trying to fix it. It has probably been over 5 years since I threw in the towel. The alarm still goes off every few weekends. I have to shut the motor off and restart it. Then I swear at it (&^&^$ Mercury). I hate that motor. I wish someone would steal it.

Does Mercury have a temp gauge that you could add to get real readings? is the pee stream hot?

SuperDave1959 wrote:

Does Mercury have a temp gauge that you could add to get real readings? is the pee stream hot?

You could just use a IR gun on the head, or even touch the head to see if it is running too hot…

Sounds like you guys need to find a new place to take your motors, after returning more then 2 times its time to find a guy that knows what he is doing and can and knows how to test the sensors before replacing them.

onestout wrote:

Still goes back to my original question, is the motor actually overheating or is it just an alarm?

When they just replaced the oil sensor and I was fishing on the Rainy this spring it was definitely overheating IMHO. There wasn’t much water coming out of the tell tale and it sounded like a tea kettle. Little to no water coming out then a blast of super hot water. Also the motor would idle down to it’s safety mode so I couldn’t go above a certain RPM. When I got back home I had the impeller replaced (which was suppose to be done the first time I took it in). First trip out the same long tone warning signal came on as soon as I opened the throttle to WO and the safety RPM governor set in. My pee stream looked fine and it didn’t feel super hot. It had only been running for 10 minutes and 90% of that was at idle speeds.

I’m going to check the warning signal wiring again as we cut it while we were fishing as we couldn’t take the sound anymore. The dealership said they reconnected the wires but I’m going to double check that. We were trolling at idle speeds and I figured I couldn’t be doing too much damage to the motor as we were in water temps in the mid 30’s. I was only using the big motor after my trolling batteries died about 1/2 through our fishing day. The problem got worse as the week went on.

If the alarm didn’t come on after the impeller replacement until you hit WOT it sounds like the alarm is working correctly (it turns on and off, normally a bad sensor is always on or always off). Have you tried backflushing to motor to get any sand or stuff out that may be hurting the water flow? If the backflush doesn’t get everything out (the issue is still present) you can pull the exhaust plate and manually clean everything thing out that may be causing the restricted flow.

steve-0 not being a smart ass here,but now that we are getting the full story and reading the wires were cut,I am lead to believe that there may be more damage than thought,maybe,maybe not.

if the dealer reconnected the wires crossed,( easy if they are the same color )
the alarm is being fed power and finding ground somewhere and may be setting a false alarm,check those wires to see if this happened.

now,if you ran it long enough while it was as you say,sounding like a tea kettle,you may have cooked it and no amount of cooling water will help,I cant tell that by not being there.

if you dont mind going to newton to have it looked at by a small independent shop,pm me and I will give you a number to call,I used to work for this guy and he does top notch work,in fact,if he needs me,all he has to do is call me.

it will be taken to the water and run just like you would to find the problem,no test tanks there that can give false readings,it will be tested in a real world scenario.

onestout wrote:

If the alarm didn’t come on after the impeller replacement until you hit WOT it sounds like the alarm is working correctly (it turns on and off, normally a bad sensor is always on or always off). Have you tried backflushing to motor to get any sand or stuff out that may be hurting the water flow? If the backflush doesn’t get everything out (the issue is still present) you can pull the exhaust plate and manually clean everything thing out that may be causing the restricted flow.

After checking the thermostat yesterday I reinstalled it and back flushed the motor. I can’t get the boat back out on the water until next week to see if that did any good.

PM sent Iowaboy1

Iowaboy1 wrote:

steve-0 not being a smart ass here,but now that we are getting the full story and reading the wires were cut,I am lead to believe that there may be more damage than thought,maybe,maybe not.

if the dealer reconnected the wires crossed,( easy if they are the same color )
the alarm is being fed power and finding ground somewhere and may be setting a false alarm,check those wires to see if this happened.

now,if you ran it long enough while it was as you say,sounding like a tea kettle,you may have cooked it and no amount of cooling water will help,I cant tell that by not being there.

if you dont mind going to newton to have it looked at by a small independent shop,pm me and I will give you a number to call,I used to work for this guy and he does top notch work,in fact,if he needs me,all he has to do is call me.

it will be taken to the water and run just like you would to find the problem,no test tanks there that can give false readings,it will be tested in a real world scenario.

Steve-O ,didnt get it yet,but I sent you the name and number.

it would be good for everyone if you post what is found out,someone else can and will have the same problem as you as these motors age,its bound to happen I promise you.
best of luck!!!!!!!!!!!

Iowaboy1 wrote:

Steve-O ,didnt get it yet,but I sent you the name and number.

it would be good for everyone if you post what is found out,someone else can and will have the same problem as you as these motors age,its bound to happen I promise you.
best of luck!!!!!!!!!!!

Once I get it figured out I’ll definitely post what the issue was. Thanks again for all your help.

A quick update. I took the boat out fishing last week. I was more concerned with fishing as I didn’t need my big motor for fishing, just launching. After fishing some spots close to the launch I drove just above idle to another spot. After driving for 10-15 minutes I reached my spot. I was using the big motor to find the exact spot I wanted to sit on before hitting my spot lock on the Minnkota. The overheat alarm went off. I would touch the throttle control and the signal would stop for a second and then start again. I turned off the motor and used the Minnkota to hold my spot. I fished the spot for 20 minutes and headed back down lake. Started the motor and the warning signal started again. I’d turn off the motor start it again same thing would happen. I idled up to just below wake speed and the warning signal turned off. Once I got to open water (I was fishing in a lot of submerged timber) I throttled all the way up to WO and ran down and back the length of lake which took about 15 minutes. It ran like it should and I felt the water coming out the pee hole after doing this and it felt fine. Before the trip I checked the wiring around the warning signal in the ignition switch. We had cut the wires to the signal on our Rainy River fishing trip. The shop had repaired that but there were a few exposed wires that I’d painted over with liquid electrical tape. Does it sound like there still could be problems with the wiring? I would barely touch the throttle control and the signal would shut off for just a second.

Steve,I just went through this myself with a friends 75 hp mercury,the module that the alarms are hooked to was bad.

unhook all of your sensors,with the key on engine OFF,let it sit for as long as it takes and see if the alarm comes on by itself,if it does,the module is shot.

on his motor,the module sits down low to your right as you are facing the drivers side of the motor.

if the alarm does not come on,hook the sensors back up one at a time until the alarm sounds,the sensor that causes it to come on is your culprit.
mind you,the module that was bad sounded steady just like the temp sensor would.

I talked to Rick about yours also,if in fact yours did overheat last year,it most likely took out the sensor,from what I gathered from him,the temps sensors are weak from the get go and it does not take much to cause them to sound the alarm prematurely once they have gotten hot,it will take a new one to fix it if that is what happened to yours.

forgot to add this,the oil pressure switch will cause the alarm to sound once you hook it back up,it is designed to sound the alarm when there is no oil pressure.
the engine will have to be started to test it.

dont let it fool you into thinking it is bad again unless it was junk out of the box when it was installed which you will figure out once everything else is checked.

Thanks for the reply Iowaboy1. Next chance I get I’ll start looking at what you mentioned. I appreciate your help.

Update on my ongoing issue. I ordered a new heat sensor and attempted to install it Friday after work. The old sensor came out with no problem. Tried screwing in the new sensor and I couldn’t get it threaded. I was being deliberate and taking my time. After several attempts with no luck I got the old sensor and screwed it back in by hand. I tried unscrewing it by hand and no luck so I grabbed my open ended wrench and lightly turned it and and that’s when my 5 minute job turned into a nightmare. The sensor broke off in the hole. I tried using a screw extractor but it just ate up the plastic. So today I bought some brushes and gently cleaned out the threads. I talked to a friend of mine who’s more mechanical than I and we both thought if we got a 10mm bolt (that’s the size thread on the sensor) we could slowly work this in and clean as we went. Turn it by hand and then a 1/4 turn with wrench, screw back out, clean hole with shopvac, repeat. We did this until we thought we had enough room to install the new sensor. It worked great until we had to turn it with a wrench for that final last 1/2 turn and snap… it broke off again. Do I try the same method again and just go farther with the bolt or do I try to re-tap the threads? I just wanna go fishn’…

Hopefully this is my final update on my Mercury 40 4-stroke. After breaking off the sensor again I ordered a thread cleaning tap from Snap-On. I couldn’t get the tap started but I noticed I had some clean threads on the back side of the exhaust cover. After removing the cover I was able to clean the threads out with the tap and install a new temp. sensor. Glad I did that as there was quit a bit of debris in chamber that could have caused more problems. As I was reinstalling the 10 bolts using my torque wrench (which is no small feat) I snapped off a bolt. I ended up snapping off a 2nd bolt in the process. Looks like my torque wrench was not acting properly. I removed the cover again and extracted the two broken off bolts (once again, no small feat). I decided then to order 10 new bolts, 2 new gaskets. I’ve learned over this process if you’re replacing one part you should replace all the parts around that area. I hooked up the motor to a hose to back flush again. After that I hooked up the muffs and ran for 20-30 minutes with no issue. Of course running it on muffs doesn’t really tell you much until you put it under a load I’ve learned. I fished yesterday with no issue. I trolled for several hours with the big motor and all sounded and looked fine. I wasn’t able to run it wide open like I had planned as some wx came in and we got off the water.

Thanks for all the reply’s this site is a true resource. Thanks Iowaboy1 your last bit of information helped me diagnose the problem. Bad heat sensor.