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Discussion Starter · #1 ·
Hi folks,

My 2006 Ninja 650r had the dreaded water pump seal failure - started dripping coolant from the weep hole, followed by boiling noises in the radiator.

I took it apart today - the impeller was extremely difficult to remove and I ended up damaging it. After pulling it and the flat-ish plate/housing that holds the mechanical seal, I found milky fluid and a good amount of gunk behind the flat housing.

The milky fluid I don't think is surprising - some coolant mixed with oil here. But, the gunk on the bottom here surprised me. Most of it clears out easily by wiping; around the impeller though it was solidified into a hard, plastic-like substance.

See photos below - am I good to just clean this out as best I can, replace the water seal + oil seal + impeller as typical, and go on my way? Or is there any concern that this gunk is in places it shouldn't be?

(When I drained the engine oil, it looked good - no milkiness etc.)





Thank you!
 

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Good call motocopter.
Crowded, if you’re not the original owner, a PO might have poured radiator sealer in. Or perhaps the wrong type coolant was used.
I’ve never seen that gunk before in a water pump.
You need coolant specific for aluminum engines or it will cause corrosion. That gunk could be corrosion.
Hard water can cause it too. Only distilled water should be used.

If that were my bike, since the system is apart, I would inspect every inch of it for more gunk. Especially the radiator. Then consider a flush.
 

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For sure. Inspect the radiator.

I was suspecting that if that sludge were found in the hoses, then @CrowdedTrousers would keep looking.
Any evidence of corrosion I have ever found in a motorcycle engine is usually a white fuzzy substance floating in the old coolant, not that yellow gunk. That looks to me like some sort of stop-leak but I’m not familiar with that stuff.
 

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Discussion Starter · #7 ·
Thanks everyone for the suggestions - good to know this is not typical gunk. I am not the original owner; tomorrow I can inspect the hoses and check out the radiator.

Ive never taken a bike radiator off - guessing I can only inspect the inlet and outlet, but I'll try to do that.

If I find more of this gunk - I'm guessing I should do a flush with distilled water? (Once the pump is back together and such?)
 

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There’s specific stuff and a specific procedure to flush the system. Whatever you use needs to be run through the system by running the bike and getting it hot, then flushing the flush chemical out of the system using distilled water. So the water pump needs to be repaired.
You can buy distilled water at the grocery store in the water isle and it costs about the same as a gallon of generic drinking water.
 

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Discussion Starter · #9 ·
Thanks Zed and folks, yesterday I pulled all the hoses and inspected everything cooling-related I could get to. Found some good news and some strange news.

The good news: I didn't find any traces of more gunk or corrosion/fuzz in the hoses, the expansion tank, the 3 locations on the radiator I was able to look in, or the location where coolant enters the engine. All the hoses look to be in great shape; I cleaned out the hoses and minor dust/dirt in the expansion tank, and put it back together.

The strange news: the (remaining) coolant I drained out a few days ago has been sitting in the drain pan, and when I went to inspect the hoses and such last night, the entire thing has become gelatinous - see picture below. Doing some googling, I read that certain coolants can get "Silicate dropout" when they get old, turning into a gel. (my garage has been 50-65 deg F... not super cold)

The interesting thing is - when I drained it, the coolant was entirely liquid - no gel or chunks. It was mostly clear, not a lot of green. And when taking the hoses and such out, all I found was residual liquid, no gel. In case it's relevant - the bike has been sitting for ~1.5 years.

Not entirely sure what all this means but - I'm thinking a flush would not be a bad idea. Reading the service manual, it instructs "Fill the cooling system with fresh water mixed with a flush-ing compound. Do not use a flushing compound which is harmful to the aluminum engine and radiator."

Do you folks agree a flush would be good, and any suggestions for flushing products + a good coolant to use?
Thanks!

Dishware Liquid Cookware and bakeware Fluid Serveware


(touching it with fingers):
Liquid Fluid Chemical compound Water Monochrome photography
 

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WOW, Happy new year.
I'm pretty sure that stuff was a radiator stop-leak product. It doesn't solidify until contact with air. That’s how it knows it found the leak. (Google 'liquid glass').
I would absolutely flush the system very carefully and thoroughly. There’s probably ten thousand videos on YouTube. And I’d take another look in that radiator.
I do know you leave the flush in for a short while while riding the bike, then you have to ‘neutralize' the flush, then you have to flush the neutralized flush out. There’s usually a separate product for each step. Then fill the system with pre-mix coolant or the type you mix with distilled water. It’s a PITA.

But make sure you use a flush that flushes out 'stop-leak' instead of just regular gunk or whatever it is that clogs coolant systems.

Also, could you save that bowl of gunk? I’m just wondering how solid it gets over time exposed to air. Thanks.

EDIT: You might contact a local radiator repair shop on how to flush out stop-leak.
 

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Discussion Starter · #12 ·
WOW, Happy new year.
I'm pretty sure that stuff was a radiator stop-leak product. It doesn't solidify until contact with air. That’s how it knows it found the leak. (Google 'liquid glass').
I would absolutely flush the system very carefully and thoroughly. There’s probably ten thousand videos on YouTube. And I’d take another look in that radiator.
I do know you leave the flush in for a short while while riding the bike, then you have to ‘neutralize' the flush, then you have to flush the neutralized flush out. There’s usually a separate product for each step. Then fill the system with pre-mix coolant or the type you mix with distilled water. It’s a PITA.

But make sure you use a flush that flushes out 'stop-leak' instead of just regular gunk or whatever it is that clogs coolant systems.

Also, could you save that bowl of gunk? I’m just wondering how solid it gets over time exposed to air. Thanks.
EDIT: You might contact a local radiator repair shop on how to flush out stop-leak.
Thanks Zed, I'll hold onto the gunk until I need the pan again. We'll see what happens with it.

I watched the video - sounds like it can be difficult to flush out this stuff. The Irontite Thoroflush product sounds like it would definitely work, although I am a little nervous about how harsh it might be to anything else in the system. Do you think there is any risk to a bike cooling system as opposed to using it in a car?

According to the service manual at least - it seems slightly more simple to do this on a bike than a car, as there are no heater hoses/heater core etc.

I think my next steps in order are:
  1. (Wait for parts to arrive)
  2. Replace housing, mechanical water + oil seal and O-rings
  3. Flush system with distilled water and flush product (Thoroflush or something else)
  4. Flush with just distilled water
  5. Refill with coolant
  6. (Done?)
Thanks!
 

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Too bad the guy pouring the Kool-Aid mix into his Dakota doesn't tell us if his engine temperature was reduced with improved cooling. It's possible his engine already had another problem.

On another note. With concern of the radiator being clogged, how about water jackets in the head and around the cylinders? As the mixture (looks like tofu!) gels in the pan, and while awaiting parts, it would be worthwhile to determine if the coolant passages are open or clogged.
 

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My concern would be that stuff solidifying in the radiator and narrow passageways now that its exposed to air. That’s how stop leak works. It remains in a liquid state until it finds air, meaning a leak, then hardens to clog it at that spot while the rest of it just circulates in liquid form in the system. Now your empty system is full of air.

I would reassemble now to flush the system then take it apart again to fix the leaking water pump. You would also get a second look to see how clean it got.

I always think a motorcycle's coolant system is more delicate than a car only because everything is smaller. It’s like comparing a wrist watch to a grandfather clock. Your motorcycle's radiator isn’t much larger than a heater core in a car, and those can clog from this stuff.
I think, while running the bike you should put your hand on the radiator to make sure that it’s getting hot over it’s entire area. That’ll tell you it’s clear.

You definitely have a PITA on your hands but it’ll be worth the effort. My only air cooled bike is my zr7S and you better believe I surely appreciate that it doesn’t have a cooling system to deal with like my other three bikes.
 

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Discussion Starter · #15 ·
On another note. With concern of the radiator being clogged, how about water jackets in the head and around the cylinders?
Hi moto, I am not sure how I would check these. Would this require taking off a valve cover, or similar? I would prefer to avoid tearing the bike apart more than absolutely needed...

My concern would be that stuff solidifying in the radiator and narrow passageways now that its exposed to air. That’s how stop leak works. It remains in a liquid state until it finds air, meaning a leak, then hardens to clog it at that spot while the rest of it just circulates in liquid form in the system. Now your empty system is full of air.

I would reassemble now to flush the system then take it apart again to fix the leaking water pump. You would also get a second look to see how clean it got.

I always think a motorcycle's coolant system is more delicate than a car only because everything is smaller. It’s like comparing a wrist watch to a grandfather clock. Your motorcycle's radiator isn’t much larger than a heater core in a car, and those can clog from this stuff.
I think, while running the bike you should put your hand on the radiator to make sure that it’s getting hot over it’s entire area. That’ll tell you it’s clear.
Thanks zed - as I was taking things off the other day, and finding liquid, it occurred to me that if exposure to air is what does it - I need to work fast. I took everything apart and then reassembled it within 30 minutes, plugging up holes for the missing water pump, but yes there is no fluid in it right now. I could fill it with water while waiting on parts to arrive. Would expect everything to get here within a week.

When you say reassemble now to flush the system - I can't flush it without a water pump, right?
 

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Yes, you need the water pump to circulate the mixture. You need to start and run the bike. I was suggesting doing the procedure with the leaky pump seal providing no water gets inside the crankcase. Just to do it now.
You‘lol know if the radiator is clogged if it doesn’t heat up completely.
If the radiator was off the bike you could fill it with hot water in the sink to make sure all passages are clear.
 

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Discussion Starter · #17 ·
Yes, you need the water pump to circulate the mixture. You need to start and run the bike. I was suggesting doing the procedure with the leaky pump seal providing no water gets inside the crankcase. Just to do it now.
You‘lol know if the radiator is clogged if it doesn’t heat up completely.
If the radiator was off the bike you could fill it with hot water in the sink to make sure all passages are clear.
Got it - I'm afraid that won't be possible right now since the impeller was so stuck on there, it got bent+damaged when removing it. I think I'll have to wait til parts get here - or pull the radiator off if that's the area of greatest concern. If I pour a pot of boiling water into the top of the radiator (while on the bike) - would it work its way through the passages, or does it need pressure behind it?
 

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If you can take the radiator off, try keeping it submerged in a tray of water so that if stop leak is in there, it may not gunk up.
With the radiator out, you can pour hot water in one end and see that it flows evenly through the radiator tubes.
And you might try experimenting with the gunk you have saved. Maybe regular dish soap or some other household cleaner will dissolve it. Then you can soak the radiator in it.
 

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Discussion Starter · #19 ·
If you can take the radiator off, try keeping it submerged in a tray of water so that if stop leak is in there, it may not gunk up.
With the radiator out, you can pour hot water in one end and see that it flows evenly through the radiator tubes.
And you might try experimenting with the gunk you have saved. Maybe regular dish soap or some other household cleaner will dissolve it. Then you can soak the radiator in it.
Thanks Zed. I pulled the radiator tonight; tried running tap water through it from both ends - it came out readily at both ends and did not appear to be impeded from what little I could tell. It is now sitting submerged in water. I capped the engine-side hose with plastic wrap and clamped it to keep it airtight as much as possible, to prevent any air movement possible...

Now - how much do I need to be worried about the engine passages? Some parts arrived today, but I don't think the impeller will be here for another week. I had the thought of putting a garden hose into the engine-side hose, which I think would push water through and then come out at the water pump area. Would this be a helpful idea? Anything bad with running some tap water through it (or a pot of boiling water)?

Thanks again.

Rectangle Gas Composite material Automotive radiator part Wood


Tire Bicycle frame Bicycle tire Bicycle handlebar Sports equipment
 

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Spraying a garden hose couldn’t hurt. Try it and see what and where it comes out.
The internal coolant passages and water jackets, I believe, are large enough that the stop leak won’t bother them but you got to get any remaining stop leak out to reduce the risk of clogging the radiator in the future.
Youll be ok.

Also, while garden hosing, there’s usually a bolt somewhere in the system meant for bleeding air out of the system while filling. Flush that out too. And the thermostat if it’s not too much trouble.
 
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