Care and cleaning of water stones

I'm learning to sharpen tools. I bought a kit from lee valley, a combination 1000x/4000x water stone and a honing guide. Last night I was working away at my plane iron for quite a while, 'cause the blade is in bad shape (I probably should've started with something coarser than 1000x, but I have more time than resources).
As I was working, there was some black particulate matter collecting in the puddles on the stone (swarf?). I'm not sure if this is metal from the blade, or particles of the stone, or both. Periodically I would rewet the stone and rinse off most of this black stuff. Not all of it came off though, and now my 1000x stone has some black swirly patterns on it, like a good cheescake, and I can't rinse them off or rub them off totally with my fingers under running water.
Do I need to worry about these marks? How can I clean them? I can take photos if that would help.
Thanks, Adam
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Was there some sort of protective coating/film on your plane iron, that wasn't removed before sharpening? I'm guessing... (I've sharpened a chisel with lacquer still on using a diamond stone and it put some nice streaks on the stone, but those came off because a diamond stone isn't porous.) You may have imbedded some of the dirty film into your stone, and if so my first suggestion would be to flatten the stone.
I have the small 1000x/4000x stone (same kit; I outgrew it very quickly), and the coarse side doesn't generate very black swarf. The fine side does, and yes, I rinse off periodically.
Find a copy of Fine Woodworking #169 (April 2004) and read the article on waterstones. I was getting inconsistent flattening results until I started doing what they said.
Jacobe Hazzard wrote:

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Daniel H wrote:

On further examination the black substance was coming from the brass roller cam, was mixing with the swarf and leaving trails that followed the blade edges. After careful cleaning of the brass hardware, the blade and the stone, followed by continued use of the stone with frequent rinsing, I've managed to clean out the marks completely. I'm not sure where the black stuff came from initially, it may have been from the product I used to lubricate the roller cam (a natural oil with a Teflon additive), I'll try again with mineral oil.

The good news is the bevel finally looks great! After honing until my fingers wrinkled from moisture (note to self: gloves next time) and then honing three times as much more, I've taken out the rust and the chips and the weird contours. I'm all set to hone the micro bevel, but I thought it wise to have a go at that when I'm fresh tomorrow
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On Fri, 29 Oct 2004 02:07:44 -0400, Jacobe Hazzard wrote:

NO. Don't put oil on or near your waterstone. Don't even use wax on the guide's threads (damhikt). Dry lube appears to work, so far. Remember, this is a _water_ stone, not an _oil_ stone.
--
"Keep your ass behind you"


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Australopithecus scobis wrote:

What's dry lube? Graphite?
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On Fri, 29 Oct 2004 20:03:42 -0400, Jacobe Hazzard wrote:

Probably. The squeeze bottle I use is at least 40 years old. Some salesman's sample that's followed me around all these years. If it ever runs out, I have a new tube of graphite powder waiting...
--
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Jacobe Hazzard wrote:

Oil is dangerous to a waterstone. I lubricate my roller but I use very small amounts of wd-40 and I blow as much water out before and lubricant out afterwards as I can with a blower ("compressed air", or actually, R-134A refridgerant). My honing guide is essentially free of any oil on any exposed surface before I use it.
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